ERS2536336 SAMEA4716187 9606 Homo sapiens Protocols: ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. MCF-10A (ATCC CRL-10317) was cultured in Mammary Epithelial Cell Growth Medium (MEGM BulletKit, Lonza, Catalog No. CC-3150) with added 100 ng/ml cholera toxin. None ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. Cells were treated with ICI 182,780 10-7 M for 3 days and with EPZ004777 6.4 µM or DMSO for 3 and 6 days. Conversion from BCL to fastq was perfromed using BCL2Fastq 104cells/well were incubated with compounds for 3 or 6 days with media containing compounds or vehicle and in particular MCF-7 cells treated with EPZ004777 6.4µM or DMSO for for 3 and 6 days or with 4-hydroxytamoxifen 10-7 M (4-OHT) or fulvestrant 10-7 M (ICI 182,780) or DMSO for 3 days. LCC2 cells were treated with 4-hydroxytamoxifen 10-7 M (4-OHT) or DMSO for 3 days and medium replaced every 2 days. Medium was replaced every 2 days. Total RNA was extracted using standard RNA extraction method with TRIzol (Invitrogen). 0.3-0.4 mL of TRIzol™ Reagent per 1 × 105-107cells was added directly to the culture dish to lyse the cells pipetting several times to homogenize. Then was added 0.1 ml of 1-Bromo-3-chloropropane (Sigma- Aldrich) and after incubation of 2-3 minutes, the samples was centrifugated for 15 minutes at 12,000 × g at 4°C. Then, the aqueous phase, containing the RNA, was collected into a new tube and precipitate with isopropanol and resuspended in RNAse/DNase free water. Nascent RNA was extracted from each sample as described by Khodor et al. In brief, following TRIzol (Life Techonolgies) addition, samples were incubated at 65°C to dissolve DNA-Histone-Pol II-RNA pellets and RNA was extracted following the manufacturer's protocol. For sequencing, indexed libraries were prepared using 1 µg of Nascent RNA as starting material, with TruSeq Stranded Total RNA Sample Prep Kit (Illumina Inc.). ENA-FIRST-PUBLIC 2019-02-08T17:04:04Z ENA-LAST-UPDATE 2018-06-07T16:31:53Z External Id SAMEA4716187 INSDC center name Laboratory of Molecular Medicine and Genomics INSDC first public 2019-02-08T17:04:04Z INSDC last update 2018-06-07T16:31:53Z INSDC status public Submitter Id E-MTAB-6871:Sample 1 broker name ArrayExpress cell line MCF-7 cell type mammary epithelial cell common name human disease invasive ductal carcinoma metastatic site pleural effusion organism part mammary gland sample name E-MTAB-6871:Sample 1 scientific_name Homo sapiens ERS2536337 SAMEA4716188 9606 Homo sapiens Protocols: ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. MCF-10A (ATCC CRL-10317) was cultured in Mammary Epithelial Cell Growth Medium (MEGM BulletKit, Lonza, Catalog No. CC-3150) with added 100 ng/ml cholera toxin. None ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. Cells were treated with ICI 182,780 10-7 M for 3 days and with EPZ004777 6.4 µM or DMSO for 3 and 6 days. Conversion from BCL to fastq was perfromed using BCL2Fastq 104cells/well were incubated with compounds for 3 or 6 days with media containing compounds or vehicle and in particular MCF-7 cells treated with EPZ004777 6.4µM or DMSO for for 3 and 6 days or with 4-hydroxytamoxifen 10-7 M (4-OHT) or fulvestrant 10-7 M (ICI 182,780) or DMSO for 3 days. LCC2 cells were treated with 4-hydroxytamoxifen 10-7 M (4-OHT) or DMSO for 3 days and medium replaced every 2 days. Medium was replaced every 2 days. Total RNA was extracted using standard RNA extraction method with TRIzol (Invitrogen). 0.3-0.4 mL of TRIzol™ Reagent per 1 × 105-107cells was added directly to the culture dish to lyse the cells pipetting several times to homogenize. Then was added 0.1 ml of 1-Bromo-3-chloropropane (Sigma- Aldrich) and after incubation of 2-3 minutes, the samples was centrifugated for 15 minutes at 12,000 × g at 4°C. Then, the aqueous phase, containing the RNA, was collected into a new tube and precipitate with isopropanol and resuspended in RNAse/DNase free water. Nascent RNA was extracted from each sample as described by Khodor et al. In brief, following TRIzol (Life Techonolgies) addition, samples were incubated at 65°C to dissolve DNA-Histone-Pol II-RNA pellets and RNA was extracted following the manufacturer's protocol. For sequencing, indexed libraries were prepared using 1 µg of Nascent RNA as starting material, with TruSeq Stranded Total RNA Sample Prep Kit (Illumina Inc.). ENA-FIRST-PUBLIC 2019-02-08T17:04:04Z ENA-LAST-UPDATE 2018-06-07T16:31:53Z External Id SAMEA4716188 INSDC center name Laboratory of Molecular Medicine and Genomics INSDC first public 2019-02-08T17:04:04Z INSDC last update 2018-06-07T16:31:53Z INSDC status public Submitter Id E-MTAB-6871:Sample 2 broker name ArrayExpress cell line MCF-7 cell type mammary epithelial cell common name human disease invasive ductal carcinoma metastatic site pleural effusion organism part mammary gland sample name E-MTAB-6871:Sample 2 scientific_name Homo sapiens ERS2536338 SAMEA4716189 9606 Homo sapiens Protocols: ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. MCF-10A (ATCC CRL-10317) was cultured in Mammary Epithelial Cell Growth Medium (MEGM BulletKit, Lonza, Catalog No. CC-3150) with added 100 ng/ml cholera toxin. None ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. Cells were treated with ICI 182,780 10-7 M for 3 days and with EPZ004777 6.4 µM or DMSO for 3 and 6 days. Conversion from BCL to fastq was perfromed using BCL2Fastq 104cells/well were incubated with compounds for 3 or 6 days with media containing compounds or vehicle and in particular MCF-7 cells treated with EPZ004777 6.4µM or DMSO for for 3 and 6 days or with 4-hydroxytamoxifen 10-7 M (4-OHT) or fulvestrant 10-7 M (ICI 182,780) or DMSO for 3 days. LCC2 cells were treated with 4-hydroxytamoxifen 10-7 M (4-OHT) or DMSO for 3 days and medium replaced every 2 days. Medium was replaced every 2 days. Total RNA was extracted using standard RNA extraction method with TRIzol (Invitrogen). 0.3-0.4 mL of TRIzol™ Reagent per 1 × 105-107cells was added directly to the culture dish to lyse the cells pipetting several times to homogenize. Then was added 0.1 ml of 1-Bromo-3-chloropropane (Sigma- Aldrich) and after incubation of 2-3 minutes, the samples was centrifugated for 15 minutes at 12,000 × g at 4°C. Then, the aqueous phase, containing the RNA, was collected into a new tube and precipitate with isopropanol and resuspended in RNAse/DNase free water. Nascent RNA was extracted from each sample as described by Khodor et al. In brief, following TRIzol (Life Techonolgies) addition, samples were incubated at 65°C to dissolve DNA-Histone-Pol II-RNA pellets and RNA was extracted following the manufacturer's protocol. For sequencing, indexed libraries were prepared using 1 µg of Nascent RNA as starting material, with TruSeq Stranded Total RNA Sample Prep Kit (Illumina Inc.). ENA-FIRST-PUBLIC 2019-02-08T17:04:04Z ENA-LAST-UPDATE 2018-06-07T16:31:53Z External Id SAMEA4716189 INSDC center name Laboratory of Molecular Medicine and Genomics INSDC first public 2019-02-08T17:04:04Z INSDC last update 2018-06-07T16:31:53Z INSDC status public Submitter Id E-MTAB-6871:Sample 3 broker name ArrayExpress cell line MCF-7 cell type mammary epithelial cell common name human disease invasive ductal carcinoma metastatic site pleural effusion organism part mammary gland sample name E-MTAB-6871:Sample 3 scientific_name Homo sapiens ERS2536339 SAMEA4716190 9606 Homo sapiens Protocols: ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. MCF-10A (ATCC CRL-10317) was cultured in Mammary Epithelial Cell Growth Medium (MEGM BulletKit, Lonza, Catalog No. CC-3150) with added 100 ng/ml cholera toxin. None ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. Cells were treated with ICI 182,780 10-7 M for 3 days and with EPZ004777 6.4 µM or DMSO for 3 and 6 days. Conversion from BCL to fastq was perfromed using BCL2Fastq 104cells/well were incubated with compounds for 3 or 6 days with media containing compounds or vehicle and in particular MCF-7 cells treated with EPZ004777 6.4µM or DMSO for for 3 and 6 days or with 4-hydroxytamoxifen 10-7 M (4-OHT) or fulvestrant 10-7 M (ICI 182,780) or DMSO for 3 days. LCC2 cells were treated with 4-hydroxytamoxifen 10-7 M (4-OHT) or DMSO for 3 days and medium replaced every 2 days. Medium was replaced every 2 days. Total RNA was extracted using standard RNA extraction method with TRIzol (Invitrogen). 0.3-0.4 mL of TRIzol™ Reagent per 1 × 105-107cells was added directly to the culture dish to lyse the cells pipetting several times to homogenize. Then was added 0.1 ml of 1-Bromo-3-chloropropane (Sigma- Aldrich) and after incubation of 2-3 minutes, the samples was centrifugated for 15 minutes at 12,000 × g at 4°C. Then, the aqueous phase, containing the RNA, was collected into a new tube and precipitate with isopropanol and resuspended in RNAse/DNase free water. Nascent RNA was extracted from each sample as described by Khodor et al. In brief, following TRIzol (Life Techonolgies) addition, samples were incubated at 65°C to dissolve DNA-Histone-Pol II-RNA pellets and RNA was extracted following the manufacturer's protocol. For sequencing, indexed libraries were prepared using 1 µg of Nascent RNA as starting material, with TruSeq Stranded Total RNA Sample Prep Kit (Illumina Inc.). ENA-FIRST-PUBLIC 2019-02-08T17:04:04Z ENA-LAST-UPDATE 2018-06-07T16:31:53Z External Id SAMEA4716190 INSDC center name Laboratory of Molecular Medicine and Genomics INSDC first public 2019-02-08T17:04:04Z INSDC last update 2018-06-07T16:31:53Z INSDC status public Submitter Id E-MTAB-6871:Sample 4 broker name ArrayExpress cell line MCF-7 cell type mammary epithelial cell common name human disease invasive ductal carcinoma metastatic site pleural effusion organism part mammary gland sample name E-MTAB-6871:Sample 4 scientific_name Homo sapiens ERS2536340 SAMEA4716191 9606 Homo sapiens Protocols: ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. MCF-10A (ATCC CRL-10317) was cultured in Mammary Epithelial Cell Growth Medium (MEGM BulletKit, Lonza, Catalog No. CC-3150) with added 100 ng/ml cholera toxin. None ER-alpha positive BC cells: MCF-7 (ATCC HTB-22) were propagated in Dulbecco's modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml amphotericin-B. Cells were treated with ICI 182,780 10-7 M for 3 days and with EPZ004777 6.4 µM or DMSO for 3 and 6 days. Conversion from BCL to fastq was perfromed using BCL2Fastq 104cells/well were incubated with compounds for 3 or 6 days with media containing compounds or vehicle and in particular MCF-7 cells treated with EPZ004777 6.4µM or DMSO for for 3 and 6 days or with 4-hydroxytamoxifen 10-7 M (4-OHT) or fulvestrant 10-7 M (ICI 182,780) or DMSO for 3 days. LCC2 cells were treated with 4-hydroxytamoxifen 10-7 M (4-OHT) or DMSO for 3 days and medium replaced every 2 days. Medium was replaced every 2 days. Total RNA was extracted using standard RNA extraction method with TRIzol (Invitrogen). 0.3-0.4 mL of TRIzol™ Reagent per 1 × 105-107cells was added directly to the culture dish to lyse the cells pipetting several times to homogenize. Then was added 0.1 ml of 1-Bromo-3-chloropropane (Sigma- Aldrich) and after incubation of 2-3 minutes, the samples was centrifugated for 15 minutes at 12,000 × g at 4°C. Then, the aqueous phase, containing the RNA, was collected into a new tube and precipitate with isopropanol and resuspended in RNAse/DNase free water. Nascent RNA was extracted from each sample as described by Khodor et al. In brief, following TRIzol (Life Techonolgies) addition, samples were incubated at 65°C to dissolve DNA-Histone-Pol II-RNA pellets and RNA was extracted following the manufacturer's protocol. For sequencing, indexed libraries were prepared using 1 µg of Nascent RNA as starting material, with TruSeq Stranded Total RNA Sample Prep Kit (Illumina Inc.). ENA-FIRST-PUBLIC 2019-02-08T17:04:04Z ENA-LAST-UPDATE 2018-06-07T16:31:53Z External Id SAMEA4716191 INSDC center name Laboratory of Molecular Medicine and Genomics INSDC first public 2019-02-08T17:04:04Z INSDC last update 2018-06-07T16:31:53Z INSDC status public Submitter Id E-MTAB-6871:Sample 5 broker name ArrayExpress cell line MCF-7 cell type mammary epithelial cell common name human disease invasive ductal carcinoma metastatic site pleural effusion organism part mammary gland sample name E-MTAB-6871:Sample 5 scientific_name Homo sapiens