ERS10392720 SAMEA12786544 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786544 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-KO_Flag-UBF1-Rep1 broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/ER-Cre+/+/p53-/-/3xFLAG-ubtf1+ sample name E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-KO_Flag-UBF1-Rep1 ERS10392721 SAMEA12786545 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786545 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-KO_Flag-UBF1-Rep2 broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/ER-Cre+/+/p53-/-/3xFLAG-ubtf1+ sample name E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-KO_Flag-UBF1-Rep2 ERS10392722 SAMEA12786546 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786546 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-KO_Flag-UBF2-Rep1 broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/ER-Cre+/+/p53-/-/3xFLAG-ubtf1+ sample name E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-KO_Flag-UBF2-Rep1 ERS10392723 SAMEA12786547 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786547 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-KO_Flag-UBF2-Rep2 broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/ER-Cre+/+/p53-/-/3xFLAG-ubtf1+ sample name E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-KO_Flag-UBF2-Rep2 ERS10392724 SAMEA12786548 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786548 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-KO_0u broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/taf1bfl/fl/ER-Cre+/+/p53- sample name E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-KO_0u ERS10392725 SAMEA12786549 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786549 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-KO_100u broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/taf1bfl/fl/ER-Cre+/+/p53- sample name E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-KO_100u ERS10392726 SAMEA12786550 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786550 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-KO_150u broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/taf1bfl/fl/ER-Cre+/+/p53- sample name E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-KO_150u ERS10392727 SAMEA12786551 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786551 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-KO_50u broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/taf1bfl/fl/ER-Cre+/+/p53- sample name E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-KO_50u ERS10392728 SAMEA12786552 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786552 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-FL_Flag-UBF1-Rep1 broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/ER-Cre+/+/p53-/-/3xFLAG-ubtf1+ sample name E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-FL_Flag-UBF1-Rep1 ERS10392729 SAMEA12786553 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786553 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-FL_Flag-UBF1-Rep2 broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/ER-Cre+/+/p53-/-/3xFLAG-ubtf1+ sample name E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-FL_Flag-UBF1-Rep2 ERS10392730 SAMEA12786554 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786554 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-FL_Flag-UBF2-Rep1 broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/ER-Cre+/+/p53-/-/3xFLAG-ubtf1+ sample name E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-FL_Flag-UBF2-Rep1 ERS10392731 SAMEA12786555 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786555 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-FL_Flag-UBF2-Rep2 broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/ER-Cre+/+/p53-/-/3xFLAG-ubtf1+ sample name E-MTAB-11385:ChIP-Seq_Flag_MEF_UBF-FL_Flag-UBF2-Rep2 ERS10392732 SAMEA12786556 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786556 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-FL_0u broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/taf1bfl/fl/ER-Cre+/+/p53- sample name E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-FL_0u ERS10392733 SAMEA12786557 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786557 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-FL_100u broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/taf1bfl/fl/ER-Cre+/+/p53- sample name E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-FL_100u ERS10392734 SAMEA12786558 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786558 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-FL_150u broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/taf1bfl/fl/ER-Cre+/+/p53- sample name E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-FL_150u ERS10392735 SAMEA12786559 10090 Mus musculus Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Formaldehyde was quenched by addition of 125 mM Glycine and cells harvested and washed in PBS. Nuclei were isolated using an ultrasound-based nuclei extraction method (NEXSON: Nuclei Extraction by SONication) (ref: doi: 10.1093/nar/gkv1495. PubMed PMID: 26704968) with some modifications. Briefly, for all cell types, 33 million cells were resuspended in 1.5 ml of Farnham lab buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, protease inhibitors). Cell suspensions were sonicated in 15 ml polystyrene tubes (BD #352095) using 3 to 4 cycles of 15 sec on : 30 sec off at low intensity in a Bioruptor (Diagenode). After recovery of the NEXSON-isolated nuclei by centrifugation (1000g, 5 min), nuclei were resuspended in 1.5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM NaEDTA, 0.1% SDS, protease inhibitors) and sonicated for 25 min, 30 sec on : 30 sec off , at high intensity. Each immunoprecipitation (IP) was carried out using the equivalent of 16 x 106 cells as previously describe (ref: doi: 10.1371/journal.pgen.1006899. PubMed PMID: 28715449). To map Ubtf1 and Ubtf2 variants cDNAs encompassing the complete coding regions (Genbank: M61726 / M61725) were subcloned into pCDNA3-3xFLAG-C1 (N. Bisson) and verified by Sanger sequencing. The resulting pC3xFLAG-UBF1 and -UBF2 (lab. stocks #2072, #2073) constructs were used to transfect NIH3T3 or conditional ubtf (ubtffl/fl/ER-Cre+/+/p53-/-) MEFs (Herdman et al., 2017) and cultures selected with G418. In the case of NIH3T3, pools of positive clones expressing Ubtf1 or Ubtf2 at sub-endogenous levels were then subjected to parallel ChIP for FLAG-Ubtf1/2 (anti-FLAG) and total Ubtf. Essentially the same procedure was used for the MEFs except that cells were transfected with pCDNA3Hygro-3xFLAG-UBF1 and -UBF2 (lab. stocks #2273, #2274), expressing clones selected with Hygromycin and these used in ChIP experiments 5 days after ubtf inactivation by 4-HT addition or after mock inactivation to eliminate endogenous Ubtf. DNase-Seq analysis of MEFs was carried out following the published protocol (ref: doi: 10.1038/nmeth.2762. PubMed PMID: 24317252), the only modifications being adjustment of digestion levels to obtain the required fragmentation. DNA samples were quality controlled by qPCR before size selection following the published protocol. Immunoprecipitated chromatin was treated with RNaseA. The DNA was isolated using 2% NaSDS and 2mg.ml-1 Proteinase-K, phenol:chloroform extraction using glycogen as carrier and finally ethanol precipitation. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end or paired-end sequencing on an Illumina HiSeq 2500 or 4000, or NovaSeq 6000 (McGill University and Genome Quebec Innovation Centre). ENA first public 2022-02-03 ENA last update 2022-02-03 External Id SAMEA12786559 INSDC center alias Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC center name Professor, Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universite Laval. Senior Investigator, Cancer Research Centre, Universite Laval. Senior Investigator, St-Patrick Research Group in Basic Oncology, Oncology Division, Quebec University Hospital Research Centre INSDC first public 2022-02-03T16:21:42Z INSDC last update 2022-02-03T16:21:42Z INSDC status public Submitter Id E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-FL_50u broker name ArrayExpress cell line MEF cell line cell type mouse embryonic fibroblast cell common name house mouse developmental stage embryo stage genotype UBTFfl/fl/taf1bfl/fl/ER-Cre+/+/p53- sample name E-MTAB-11385:Dnase-Seq_Taf1b_MEF_Taf1b-FL_50u