ERS3138048 SAMEA5331856 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331856 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM106 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3b tumor stage individual P16 organism part cancerous urothelium sample name E-MTAB-7659:PM106 scientific_name Homo sapiens sex male ERS3138049 SAMEA5331857 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331857 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM110 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3b tumor stage individual P16 organism part cancerous urothelium sample name E-MTAB-7659:PM110 scientific_name Homo sapiens sex male ERS3138050 SAMEA5331858 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331858 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM114 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3b tumor stage individual P16 organism part cancerous urothelium sample name E-MTAB-7659:PM114 scientific_name Homo sapiens sex male ERS3138051 SAMEA5331859 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331859 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM301 age 83 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3a tumor stage individual P29 organism part cancerous urothelium sample name E-MTAB-7659:PM301 scientific_name Homo sapiens sex female ERS3138052 SAMEA5331860 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331860 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM302 age 83 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3a tumor stage individual P29 organism part cancerous urothelium sample name E-MTAB-7659:PM302 scientific_name Homo sapiens sex female ERS3138053 SAMEA5331861 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331861 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM307 age 83 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3a tumor stage individual P29 organism part urothelium sample name E-MTAB-7659:PM307 scientific_name Homo sapiens sex female ERS3138054 SAMEA5331862 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331862 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM308 age 83 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3a tumor stage individual P29 organism part urothelium sample name E-MTAB-7659:PM308 scientific_name Homo sapiens sex female ERS3138055 SAMEA5331863 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331863 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM310 age 83 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3a tumor stage individual P29 organism part urothelium sample name E-MTAB-7659:PM310 scientific_name Homo sapiens sex female ERS3138056 SAMEA5331864 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331864 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM319 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part urothelium sample name E-MTAB-7659:PM319 scientific_name Homo sapiens sex female ERS3138057 SAMEA5331865 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331865 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM320 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part cancerous urothelium sample name E-MTAB-7659:PM320 scientific_name Homo sapiens sex female ERS3138058 SAMEA5331866 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331866 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM321 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part cancerous urothelium sample name E-MTAB-7659:PM321 scientific_name Homo sapiens sex female ERS3138059 SAMEA5331867 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331867 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM322 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part cancerous urothelium sample name E-MTAB-7659:PM322 scientific_name Homo sapiens sex female ERS3138060 SAMEA5331868 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331868 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM323 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part cancerous urothelium sample name E-MTAB-7659:PM323 scientific_name Homo sapiens sex female ERS3138061 SAMEA5331869 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331869 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM324 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part cancerous urothelium sample name E-MTAB-7659:PM324 scientific_name Homo sapiens sex female ERS3138062 SAMEA5331870 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331870 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM325 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part cancerous urothelium sample name E-MTAB-7659:PM325 scientific_name Homo sapiens sex female ERS3138063 SAMEA5331871 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331871 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM326 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part cancerous urothelium sample name E-MTAB-7659:PM326 scientific_name Homo sapiens sex female ERS3138064 SAMEA5331872 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331872 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM327 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part urothelium sample name E-MTAB-7659:PM327 scientific_name Homo sapiens sex female ERS3138065 SAMEA5331873 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331873 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM328 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part urothelium sample name E-MTAB-7659:PM328 scientific_name Homo sapiens sex female ERS3138066 SAMEA5331874 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331874 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM329 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part urothelium sample name E-MTAB-7659:PM329 scientific_name Homo sapiens sex female ERS3138067 SAMEA5331875 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331875 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM330 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part urothelium sample name E-MTAB-7659:PM330 scientific_name Homo sapiens sex female ERS3138068 SAMEA5331876 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331876 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM331 age 73 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging Ta stage individual P31 organism part urothelium sample name E-MTAB-7659:PM331 scientific_name Homo sapiens sex female ERS3138069 SAMEA5331877 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331877 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM333 age 81 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P32 organism part cancerous urothelium sample name E-MTAB-7659:PM333 scientific_name Homo sapiens sex male ERS3138070 SAMEA5331878 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331878 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM334 age 81 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P32 organism part cancerous urothelium sample name E-MTAB-7659:PM334 scientific_name Homo sapiens sex male ERS3138071 SAMEA5331879 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331879 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM335 age 81 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P32 organism part cancerous urothelium sample name E-MTAB-7659:PM335 scientific_name Homo sapiens sex male ERS3138072 SAMEA5331880 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331880 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM336 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P33 organism part cancerous urothelium sample name E-MTAB-7659:PM336 scientific_name Homo sapiens sex male ERS3138073 SAMEA5331881 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331881 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM337 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P33 organism part cancerous urothelium sample name E-MTAB-7659:PM337 scientific_name Homo sapiens sex male ERS3138074 SAMEA5331882 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:45Z External Id SAMEA5331882 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:45Z INSDC status public Submitter Id E-MTAB-7659:PM338 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P33 organism part cancerous urothelium sample name E-MTAB-7659:PM338 scientific_name Homo sapiens sex male ERS3138075 SAMEA5331883 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331883 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM339 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P33 organism part urothelium sample name E-MTAB-7659:PM339 scientific_name Homo sapiens sex male ERS3138076 SAMEA5331884 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331884 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM340 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P33 organism part urothelium sample name E-MTAB-7659:PM340 scientific_name Homo sapiens sex male ERS3138077 SAMEA5331885 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331885 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM347 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P33 organism part urothelium sample name E-MTAB-7659:PM347 scientific_name Homo sapiens sex male ERS3138078 SAMEA5331886 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331886 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM349 age 77 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T4a tumor stage individual P33 organism part urothelium sample name E-MTAB-7659:PM349 scientific_name Homo sapiens sex male ERS3138079 SAMEA5331887 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331887 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM405 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3b tumor stage individual P37 organism part urothelium sample name E-MTAB-7659:PM405 scientific_name Homo sapiens sex male ERS3138080 SAMEA5331888 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331888 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM409 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3b tumor stage individual P37 organism part urothelium sample name E-MTAB-7659:PM409 scientific_name Homo sapiens sex male ERS3138081 SAMEA5331889 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331889 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM411 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3b tumor stage individual P37 organism part cancerous urothelium sample name E-MTAB-7659:PM411 scientific_name Homo sapiens sex male ERS3138082 SAMEA5331890 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331890 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM412 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3b tumor stage individual P37 organism part cancerous urothelium sample name E-MTAB-7659:PM412 scientific_name Homo sapiens sex male ERS3138083 SAMEA5331891 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331891 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM473 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM473 scientific_name Homo sapiens sex male ERS3138084 SAMEA5331892 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331892 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM474 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM474 scientific_name Homo sapiens sex male ERS3138085 SAMEA5331893 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331893 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM475 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM475 scientific_name Homo sapiens sex male ERS3138086 SAMEA5331894 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331894 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM476 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM476 scientific_name Homo sapiens sex male ERS3138087 SAMEA5331895 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331895 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM477 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM477 scientific_name Homo sapiens sex male ERS3138088 SAMEA5331896 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331896 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM478 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM478 scientific_name Homo sapiens sex male ERS3138089 SAMEA5331897 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331897 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM479 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM479 scientific_name Homo sapiens sex male ERS3138090 SAMEA5331898 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331898 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM480 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM480 scientific_name Homo sapiens sex male ERS3138091 SAMEA5331899 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331899 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM481 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM481 scientific_name Homo sapiens sex male ERS3138092 SAMEA5331900 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331900 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM482 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM482 scientific_name Homo sapiens sex male ERS3138093 SAMEA5331901 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331901 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM483 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM483 scientific_name Homo sapiens sex male ERS3138094 SAMEA5331902 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331902 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM484 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part cancerous urothelium sample name E-MTAB-7659:PM484 scientific_name Homo sapiens sex male ERS3138095 SAMEA5331903 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331903 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM485 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part urothelium sample name E-MTAB-7659:PM485 scientific_name Homo sapiens sex male ERS3138096 SAMEA5331904 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331904 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM486 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part urothelium sample name E-MTAB-7659:PM486 scientific_name Homo sapiens sex male ERS3138097 SAMEA5331905 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331905 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM487 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part urothelium sample name E-MTAB-7659:PM487 scientific_name Homo sapiens sex male ERS3138098 SAMEA5331906 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331906 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM488 age 79 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P45 organism part urothelium sample name E-MTAB-7659:PM488 scientific_name Homo sapiens sex male ERS3138099 SAMEA5331907 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331907 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM491 age 74 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T2 tumor stage individual P48 organism part cancerous urothelium sample name E-MTAB-7659:PM491 scientific_name Homo sapiens sex female ERS3138100 SAMEA5331908 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331908 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM494 age 74 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T2 tumor stage individual P48 organism part cancerous urothelium sample name E-MTAB-7659:PM494 scientific_name Homo sapiens sex female ERS3138101 SAMEA5331909 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331909 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM501 age 74 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T2 tumor stage individual P48 organism part urothelium sample name E-MTAB-7659:PM501 scientific_name Homo sapiens sex female ERS3138102 SAMEA5331910 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331910 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM509 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM509 scientific_name Homo sapiens sex female ERS3138103 SAMEA5331911 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331911 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM510 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM510 scientific_name Homo sapiens sex female ERS3138104 SAMEA5331912 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331912 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM511 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM511 scientific_name Homo sapiens sex female ERS3138105 SAMEA5331913 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331913 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM512 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM512 scientific_name Homo sapiens sex female ERS3138106 SAMEA5331914 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331914 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM513 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM513 scientific_name Homo sapiens sex female ERS3138107 SAMEA5331915 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331915 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM514 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM514 scientific_name Homo sapiens sex female ERS3138108 SAMEA5331916 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331916 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM515 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM515 scientific_name Homo sapiens sex female ERS3138109 SAMEA5331917 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331917 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM516 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM516 scientific_name Homo sapiens sex female ERS3138110 SAMEA5331918 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331918 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM517 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM517 scientific_name Homo sapiens sex female ERS3138111 SAMEA5331919 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331919 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM518 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part cancerous urothelium sample name E-MTAB-7659:PM518 scientific_name Homo sapiens sex female ERS3138112 SAMEA5331920 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331920 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM520 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part urothelium sample name E-MTAB-7659:PM520 scientific_name Homo sapiens sex female ERS3138113 SAMEA5331921 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331921 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM521 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part urothelium sample name E-MTAB-7659:PM521 scientific_name Homo sapiens sex female ERS3138114 SAMEA5331922 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331922 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM522 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part urothelium sample name E-MTAB-7659:PM522 scientific_name Homo sapiens sex female ERS3138115 SAMEA5331923 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:46Z External Id SAMEA5331923 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:46Z INSDC status public Submitter Id E-MTAB-7659:PM523 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part urothelium sample name E-MTAB-7659:PM523 scientific_name Homo sapiens sex female ERS3138116 SAMEA5331924 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331924 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM524 age 52 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T1 tumor stage individual P72 organism part urothelium sample name E-MTAB-7659:PM524 scientific_name Homo sapiens sex female ERS3138117 SAMEA5331925 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331925 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM525 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part cancerous urothelium sample name E-MTAB-7659:PM525 scientific_name Homo sapiens sex female ERS3138118 SAMEA5331926 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331926 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM526 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part cancerous urothelium sample name E-MTAB-7659:PM526 scientific_name Homo sapiens sex female ERS3138119 SAMEA5331927 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331927 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM527 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part cancerous urothelium sample name E-MTAB-7659:PM527 scientific_name Homo sapiens sex female ERS3138120 SAMEA5331928 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331928 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM528 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part cancerous urothelium sample name E-MTAB-7659:PM528 scientific_name Homo sapiens sex female ERS3138121 SAMEA5331929 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331929 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM529 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part cancerous urothelium sample name E-MTAB-7659:PM529 scientific_name Homo sapiens sex female ERS3138122 SAMEA5331930 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331930 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM530 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part cancerous urothelium sample name E-MTAB-7659:PM530 scientific_name Homo sapiens sex female ERS3138123 SAMEA5331931 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331931 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM531 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part cancerous urothelium sample name E-MTAB-7659:PM531 scientific_name Homo sapiens sex female ERS3138124 SAMEA5331932 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331932 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM532 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part cancerous urothelium sample name E-MTAB-7659:PM532 scientific_name Homo sapiens sex female ERS3138125 SAMEA5331933 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331933 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM533 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part urothelium sample name E-MTAB-7659:PM533 scientific_name Homo sapiens sex female ERS3138126 SAMEA5331934 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331934 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM534 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part urothelium sample name E-MTAB-7659:PM534 scientific_name Homo sapiens sex female ERS3138127 SAMEA5331935 9606 Homo sapiens Protocols: All tissue samples were collected in collaboration with the Clinic of Urology, Asklepios Klinik Hamburg-Barmbek, Hamburg (Germany). Urothelial carcinoma and corresponding normal bladder urothelium were collected from a total of 73 patients undergoing radical cystectomy (n=48) or transurethral resection (TUR) (n=25) between May 2013 and October 2016. After resection, entire urinary bladders were assessed by the pathologist and dissected to yield cancerous and non-cancerous tissue specimens. These were immediately transferred to pre-cooled keratinocyte serum-free medium with supplements (K-SFM Kit, Gibco®, Thermo Fisher Scientific) and kept refrigerated during transport to the laboratory. Tissue culture was performed following the protocol described by Bolenz et al., tissue samples cautiously cut into pieces of about 50-100 mg and incubation on a gelatin foam matrix (Gelfoam®, Pfizer, New York City, NY, USA) presoaked with K-SFM media, supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, and 160 µg/ml Mezlocillin Carino (Carinopharm, Elze, Germany). After adaptation to culture conditions for 24 h, explants were transferred to a separate 24-well plate and were transduced with adenoviral vectors. The explants were perfused in 500 µl of 10^8 infectious viral particle counts in formulation buffer including 10 µg/ml protamine sulfate for 60 min in the culture atmosphere. Transduced samples were returned to the gelatin foam matrix and incubated for 6 days with complete medium exchange in 3 to 4-day intervals. Specifications of the culture conditions were set on the basis of prior evaluation studies (data not shown). Viability was frequently monitored in culture media using a sensitive enzymatic lactate dehydrogenase (LDH)-release assay (CytoTox-ONE, Promega, Madison, WI, USA), following suppliers' instructions or on cryo-sections by an enzyme activity assay by visualizing mitochondrial nicotinamide adenine dinucleotide (NADH) diaphorase activity. Tissue specimens for RNA preparation were sampled in RNALater® (Ambion™, Thermo Fisher Scientific) and incubated over night at 4°C before freezing at -20°C. Total RNA was purified by homogenization of the samples in Trizol™ (Ambion™, Thermo Fisher Scientific) with the gentleMACS™ Dissociater and corresponding gentleMACS M™ Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany). A phase separation step with chloroform and a spin-column purification (peqGOLD Total RNA, VWR) including DNAse digestion was performed. RNAs were quantified with the Qubit™ RNA HS Assay Kit (Molecular Probes®, Thermo Fisher Scientific) and quality was assessed on the Agilent 2100 bioanalyzer™ (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 nano kit, according to the suppliers' instructions. Libraries were prepared automatically from 250 ng total RNA in 50 µL RNAse-free water with the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.) on the epMotion 5075 (Eppendorf, Hamburg, Germany) using the `Illumina Qualified' methods. Quality and quantity of the libraries were assessed using the DNA 1000 Kit on the Agilent 2100 bioanalyzer™ (Agilent) and the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific). ENA-FIRST-PUBLIC 2020-01-08T04:06:23Z ENA-LAST-UPDATE 2019-02-11T14:43:47Z External Id SAMEA5331935 INSDC center name Provecs Medical GmbH INSDC first public 2020-01-08T04:06:23Z INSDC last update 2019-02-11T14:43:47Z INSDC status public Submitter Id E-MTAB-7659:PM535 age 50 broker name ArrayExpress common name human developmental stage adult disease urothelial carcinoma disease staging T3 tumor stage individual P73 organism part urothelium sample name E-MTAB-7659:PM535 scientific_name Homo sapiens sex female