Cell line passage #

Maintaining Medium

Hormone Deprivation Medium

Hormone Deprivation Duration / h

E2 Brand and Catalog#

Sequencing Platform

Sequencing Type

Sequencing Depth
(Million Reads)

Library Preparaton Details

DMEM/F-12 + 10% CSS, 1% nonessential amino acids, sodium pyruvate and penicillin/streptomycin w/ daily 10nM E2

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132207

Sklias A, Herceg Z, Murr R et al, 2020

Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation

Illumina HiSeq 2500

AllPrep DNA/RNA Mini kit (Qiagen) 1 µg of RNA was processed with a TruSeq RNA library preparation kit

Controls (CTR_D0_1 - 3) found at GSE132514

Phenol red free MEM plus 5% charcoal-dextran treated FBS

Indiana University

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144580

Parker TM, et al, Cancer Research, 2020

Non-linear relationship between chromatin accessibility and estradiol-regulated gene expression

Illumina HiSeq 4000

Total RNA was prepared using RNAeasy kit from Qiagen

Dr. Benita Katzenellenbogen (University of Illinois, Urbana-Champaign, IL)

MEM Eagle w/ Hank’s salts (Sigma, M1018) supplemented with 5% HyClone calf serum (GE Healthcare, SH30072) and 20mM HEPES (ThermoFisher Scientific, BP310)

Phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum

UT Southwestern Medical Center

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109570

Murakami S et al, Mol Cancer Res, 2019

Murakami S, Li R, Nagari A, Chae M et al.

Distinct Roles for BET Family Members in Estrogen Receptor α Enhancer Function and Gene Regulation in Breast Cancer Cells

Molecular Cancer Research

Illumina HiSeq 2000

The cells were collected and total RNA was isolated using the RNeasy Plus kit. Strand-specific libraries were prepared according to the “deoxyuridine triphosphate (dUTP)” method as described previously {Zhong, 2011 #6}

Marc Lippman (University of Michigan)

DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 10 μg/ml insulin

RPMI without phenol red w/ 10% CSS, 1% penicillin/streptomycin

Dana-Farber Cancer Institute

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104985

Hinohara K et al, Cancer Cell 2018

Hinohara K, Wu HJ, Vigneau S, McDonald TO et al.

KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.

Illumina HiSeq 2000

Total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA

ATCC recommended medium

Phenol red-free equivalent medium to maintaining medium

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73663

Madak-Erdogan et al, Sci Signal, 2016

Madak-Erdogan Z, Kim SH, Gong P, Zhao YC et al.

Design of pathway preferential estrogens that provide beneficial metabolic and vascular effects without stimulating reproductive tissues.

Science Signaling

Illumina HiSeq 2000

TruSeq Stranded RNAseq Sample Prep kit.

Vehicle 0.1% EtOH

DMEM (Gibco/Life Technologies, Grand Island, NY, USA), supplemented with 5% calf serum (HyClone, Logan, UT, USA), and 100 μg/ml penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA)

Phenol red-free DMEM (Gibco/Life Technologies) plus 5% charcoal-dextrantreated calf serum

Sigma (St Louis, MO, USA)

University of Missouri

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56066

Gong et al. Nucl Receptor Signaling 2014

Gong P, Madak-Erdogan Z, Li J, Cheng J et al.

Transcriptomic analysis identifies gene networks regulated by estrogen receptor α (ERα) and ERβ that control distinct effects of different botanical estrogens.

Nuclear Receptor Signaling

Illumina HiSeq 2000

∼20 million reads per sample

TruSeq Stranded RNAseq Sample Prep kit.

Vehicle 0.1% EtOH

DMEM + 10% FBS and antibiotics

Phenol-free DMEM with 10% charcoal-stripped FBS

University of Chicago IGSB

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51403

Liu et al. Bioinformatics 2014

Liu Y, Zhou J, White KP.

RNA-seq differential expression studies: more sequence or more replication?

Illumina HiSeq 2000

Standard protocol of Qiagen RNeasy mini kit. Standard protocol of TrueSeq mRNA sample prep kit

Cells at 40% confluency before RNA extraction. Control ethanol for 24 hours.

Dr. Debra Tonetti (University of Illinois at Chicago)

RPMI + 10% FBS, 1% non-essential amino acids, 2 mM L-glutamine, 1% antibiotics penicillin-streptomycin, and 6 ng/ml human recombinant insulin

Phenol red-free RPMI 1640 media w/ 5% charcoal–dextran–stripped FBS

University of Illinois at Chicago

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108308

Speltz TE et al, ACS Chem Biol 2018

Speltz TE, Danes JM, Stender JD, Frasor J et al.

A Cell-Permeable Stapled Peptide Inhibitor of the Estrogen Receptor/Coactivator Interaction.

ACS Chemical Biology

Illumina NextSeq 500

QuantSeq 3' mRNA-Seq Library Prep kit (Lexogen)

Seeding density of 150K celsl/well in 6 well plates.

DMEM containing phenol red and supplemented with 10% serum, 2 mM L-glutamine, 50 U/ml penicillin and 50 μg/ml streptomycin (all from Life Technologies GmbH)

DMEM without phenol red (Life Technologies GmbH) and supplemented with 5% charcoal stripped heat-inactivated FBS (HyClone), 2 mM l-glutamine, 50 U/ml penicillin and 50 μg/ml streptomycin

72 (publication) or 96 (GEO)

University of Oslo

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99508

Fleischer T, Nat Commun 2017

Fleischer T, Tekpli X, Mathelier A, Wang S et al.

DNA methylation at enhancers identifies distinct breast cancer lineages.

Nature Communications

Illumina HiSeq 2000

DNA-RNA duplex was purified with ChIP DNA Clean & Concentrator Kit followed by RNAse H treatment.

Perou Laboratory at UNC Chapel Hill

9 (Rep2 & Rep3), 10 (Rep4)

DMEM/F12 media +10% FBS & 2nM GlutaMax, 15 mM HEPES, and sodium bicarbonate (Sigma; #D6434)

phenol-red free DMEM/F12 +10% charcoal dextran stripped FBS + 2mM GlutaMax +0.1% EtOH

University of North Carolina at Chapel Hill

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78167

Baran-Gale etal. RNA 2016

Baran-Gale J, Purvis JE, Sethupathy P.

An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response in MCF-7 breast cancer cells.

Illumina HiSeq 2500

Total RNA was extracted using the Norgen Total RNA Purification Kit (#17200), and RNA Integrity was measured by Agilent Bioanalyzer 2100. Libraries were generated using an Illumina TruSeq Stranded mRNA Library Prep Kit

0.083, 0.167, 0.333,
0.667, 1.333, 2.667, 5.333, 10.667, 21.333

DMEM with 10% FCS

DMEM w/o phenol red and 5% charcoal stripped FCS

Radbound University

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62789

Honkela A et al, PNAS, 2015

Honkela A, Peltonen J, Topa H, Charapitsa I et al.

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays.

Proceedings of the National Academy of Sciences

Illumina HiSeq 2000

100–250 ng total RNA was subjected rRNA depletion with the Ribo-Zero Magnetic Gold Kit and processed further for strand specific RNAseq. DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

MEM containing 5% calf serum with antibiotics

Phenol-red free media containing 5% charcoal-dextran stripped calf serum

University of California at San Diego

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67295

Stender JD et al, Mol Cell 2017

Stender JD, Nwachukwu JC, Kastrati I, Kim Y et al.

Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells.

Illumina HiSeq 2000

TruSeq Index sequencing primer (Illumina). The final product was run on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit.

AMEM supplemented with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin

Phenol red-free DMEM containing charcoal-stripped FBS, 2% L-glutamine and 1% penicillin-streptomycin

Université de Montréal

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108883

Traboulsi T et al, unpublished 2019

Role of SUMOylation in differential ERα transcriptional repression by SERMs and pure antiestrogens in breast cancer cells

Illumina NextSeq 500

KAPA Stranded RNA-seq Library Preparation Kit.

DMEM + 10% fetal calf serum

DMEM lacking phenol red and containing 5% dextran-coated charcoal-stripped FCS

Imperial College London

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78286

Harrod et al. Oncogene 2017

Harrod A, Fulton J, Nguyen VTM, Periyasamy M et al.

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer.

Illumina HiSeq 2500

TruSeq® RNA Sample Preparation Kit v2 (Illumina, UK)

Manufacturer’s instructions

Case Western Reserve University

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43070

Jin F et al, Nature, 2013

Jin F, Li Y, Dixon JR, Selvaraj S et al.

A high-resolution map of the three-dimensional chromatin interactome in human cells.

Illumina HiSeq 2000

Standard Illumina protocols

Control Untreated

Phenol red-free DMEM (Sigma-Aldrich) supplemented with 10% charcoal-stripped foetal bovine serum (Sigma-Aldrich) and 1% penicillin/streptomycin (Life Technologies)

QIMR Berghofer Medical Research Institute

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107693

Baxter E et al, Endocr Relat Cancer 2019

Baxter E, Windloch K, Kelly G, Lee JS et al.

Molecular basis of distinct oestrogen responses in endometrial and breast cancer.

Endocrine Related Cancer

Illumina NextSeq 500

Standard Illumina protocols

ATCC HTB-22; RRID: CVCL_0031

RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher)

Hormone Deprivation Medium

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3315628

Guan J et al, Cell, 2019

Guan J, Zhou W, Hafner M, Blake RA et al.

Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility.

Illumina HiSeq 4000

TruSeq Stranded Total RNA Library Prep Kit (Illumina)

ATCC HTB-133; RRID: CVCL_0553

RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher)

Hormone Deprivation Medium

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3315628

Guan J et al, Cell, 2019

Guan J, Zhou W, Hafner M, Blake RA et al.

Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility.

Illumina HiSeq 4000

TruSeq Stranded Total RNA Library Prep Kit (Illumina)

ATCC CRL-2329; RRID: CVCL_1254

RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher)

Hormone Deprivation Medium

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3315628

Guan J et al, Cell, 2019

Guan J, Zhou W, Hafner M, Blake RA et al.

Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility.

Illumina HiSeq 4000

TruSeq Stranded Total RNA Library Prep Kit (Illumina)

ATCC HTB-21; RRID: CVCL_1115

RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher)

Hormone Deprivation Medium

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3315628

Guan J et al, Cell, 2019

Guan J, Zhou W, Hafner M, Blake RA et al.

Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility.

Illumina HiSeq 4000

TruSeq Stranded Total RNA Library Prep Kit (Illumina)

ATCC HTB-127; RRID: CVCL_0619

RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher)

Hormone Deprivation Medium

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3315628

Guan J et al, Cell, 2019

Guan J, Zhou W, Hafner M, Blake RA et al.

Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility.

Illumina HiSeq 4000

TruSeq Stranded Total RNA Library Prep Kit (Illumina)

ATCC HTB-20; RRID: CVCL_0179

RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher)

Hormone Deprivation Medium

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3315628

Guan J et al, Cell, 2019

Guan J, Zhou W, Hafner M, Blake RA et al.

Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility.

Illumina HiSeq 4000

TruSeq Stranded Total RNA Library Prep Kit (Illumina)

ACC 231; RRID: CVCL_0253

RPMI medium supplemented with 10% FBS, 2mM L-Glutamine (Catalog 10440, Sigma), 1X Minimum Essential Media, Non-Essential Amino Acids (MEM NEAA, Catalog No. 11140-0500, Thermo Fisher) and 1X Antibiotic-Antimycotic (Catalog No.15240-112, Thermo Fisher)

Hormone Deprivation Medium

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3315628

Guan J et al, Cell, 2019

Guan J, Zhou W, Hafner M, Blake RA et al.

Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility.

Illumina HiSeq 4000

TruSeq Stranded Total RNA Library Prep Kit (Illumina)

8, 24, 120, 240, 360, 480, 600

Dr. Jennifer Richer, University of Colorado Anschutz Medical Campus

MEM (Thermo Fisher Scientific) + 5% FBS, 1% penicillin-streptomycin, 1x final concentration non-essential amino acids (NEAA, Thermo Fisher Scientific), and 1nM final concentration insulin (Sigma-Aldrich)

Phenol-red free MEM (Thermo Fisher Scientific, 5% charcoal-stripped fetal bovine serum (Thermo Fisher Scientific), 1% penicillin-streptomycin, and NEAA and insulin

University of Utah

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148279

Arnesen et al. Cancer Research 2020

S Arnesen, Z Blanchard, MM Williams et al.

Estrogen receptor alpha mutations in breast cancer cells cause gene expression changes through constant activity and secondary effects

Illumina HiSeq 2500

KAPA Stranded mRNA-seq kit

Vehicle 0.1% DMSO (Fisher Scientific)

8, 24, 120, 240, 360, 480, 600

RPMI 1640 media (Thermo Fisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillinstreptomycin (Thermo Fisher Scientific)

Phenol-red free RPMI (Thermo Fisher Scientific), 10% charcoal-stripped fetal bovine serum, and 1% penicillin-streptomycin

University of Utah

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148279

Arnesen et al. Cancer Research 2020

S Arnesen, Z Blanchard, MM Williams et al.

Estrogen receptor alpha mutations in breast cancer cells cause gene expression changes through constant activity and secondary effects

Illumina HiSeq 2500

KAPA Stranded mRNA-seq kit

Vehicle 0.1% DMSO (Fisher Scientific)

DMEM supplemented with Penstrep and L-glutamine and 10% FBS

Phenol-red free medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS and 1% PS

Dana Farber Cancer Institute

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94493

Jeselsohn et al. Cancer Cell 2018

Jeselsohn R, Bergholz JS, Pun M, Cornwell M et al.

Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations.

Illumina NextSeq 500

Illumina Truseq RNAseq v2 kit (15025063)

Control Untreated

RPMI supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin (P/S)

Phenol-red free medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS and 1% PS

Dana Farber Cancer Institute

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94493

Jeselsohn et al. Cancer Cell 2018

Jeselsohn R, Bergholz JS, Pun M, Cornwell M et al.

Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations.

Illumina NextSeq 500

Illumina Truseq RNAseq v2 kit (15025063)

Control Untreated

Phenol-red-free IMEM with 5%

University of Pittsburgh

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89888

Bahreini et al. BCR 2017

Bahreini A, Li Z, Wang P, Levine KM et al.

Mutation site and context dependent effects of ESR1 mutation in genome-edited breast cancer cell models.

Breast Cancer Research

Illumina HiSeq 2500

TruSeq Stranded Total RNA Library Prep Kit

ATCC/NCI Breast Cancer SPORE program

RPMI 1640+10% FBS

Phenol-red-free IMEM with 10%

University of Pittsburgh

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89888

Bahreini et al. BCR 2017

Bahreini A, Li Z, Wang P, Levine KM et al.

Mutation site and context dependent effects of ESR1 mutation in genome-edited breast cancer cell models.

Breast Cancer Research

Illumina HiSeq 2500

TruSeq Stranded Total RNA Library Prep Kit

RPMI 1640 supplemented with 10% FBS and 1% penicillin-streptomycin

Phenol red–free RPMI 1640 supplemented with charcoal-stripped FBS and 1% penicillin-streptomycin

Ben May Department for Cancer Research

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80366

Singhal H et al, Sci Adv 2016

Singhal H, Greene ME, Tarulli G, Zarnke AL et al.

Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer.

Science Advances

Illumina HiSeq 2500

Used as control to T47D cell line in publication

RPMI 1640 supplemented with 10% FBS and 1% penicillin-streptomycin

Phenol red–free RPMI 1640 supplemented with charcoal-stripped FBS and 1% penicillin-streptomycin

Ben May Department for Cancer Research

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80366

Singhal H et al, Sci Adv 2016

Singhal H, Greene ME, Tarulli G, Zarnke AL et al.

Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer.

Science Advances

Illumina HiSeq 2500

1.4 billion 50-bp single-end DNA-seq reads

RPMI 1640 supplemented with 10% FBS and 1% penicillin-streptomycin

Phenol red–free RPMI 1640 supplemented with charcoal-stripped FBS and 1% penicillin-streptomycin

Ben May Department for Cancer Research

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80366

Singhal H et al, Sci Adv 2016

Singhal H, Greene ME, Tarulli G, Zarnke AL et al.

Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer.

Science Advances

Illumina HiSeq 2500

Used as control to T47D cell line in publication

RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin

48 h in RPMI supplemented with 10% charcoal-treated FBS and synchronized in G0/G1 by 16 h of serum starvation

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53463

Le Dily F et al, Genes Dev 2014

Le Dily F, Baù D, Pohl A, Vicent GP et al.

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation.

Genes & Development

Illumina HiSeq 2000

mRNA-Seq sample prep kit (ref. RS-930-1001, Illumina)

Control Untreated

RPMI1640 with L-Glutamine (Mediatech) supplemented with 10% FBS, glucose to 4.5 g/L (Sigma), 10 mM HEPES (GenDEPOT), 1 mM sodium pyruvate (GenDEPOT), and 50 μg/mL gentamycin (GenDEPOT)

RPMI1640 without phenol red and 10% charcoal-stripped FBS

Baylor College of Medicine

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116170

Lei et al. Cell Reprots 2018

Lei JT, Shao J, Zhang J, Iglesia M et al.

Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer.

Illumina HiSeq 2500

Illumina TruSeq Stranded mRNA-Seq Sample Prep kit

Control Untreated

MEM containing 10% FBS

MEM containing 10% CD-FBS

University of Illinois Urbana-Champaign

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108304

Yu et al. Cancer Letters 2019

Yu L, Wang L, Mao C, Duraki D et al.

Estrogen-independent Myc overexpression confers endocrine therapy resistance on breast cancer cells expressing ERαY537S and ERαD538G mutations.

Illumina HiSeq 4000

TruSeq Stranded mRNAseq Sample Prep kit (Illumina)

RPMI-1640 (Invitrogen) supplemented with 1% penicillin-streptomycin (Invitrogen) and 10% FBS (HyClone)

Phenol red-free RPMI-1640 supplemented with 10% dextran/charcoal treated fetal bovine serum

HudsonAlpha Institute

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38234

Gertz J, et al. Genome Res, 2012

Gertz J, Reddy TE, Varley KE, Garabedian MJ et al.

Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner.

Genome Research

Illumina HiSeq 2000

"We obtained at least 30 million reads that aligned to RefSeq transcripts"

Double-stranded cDNA was constructed from the DNase-treated mRNA. Fifty ng cDNA then underwent Nextera tagmentation and PCR. Libraries were constructed with DNA barcodes and pooled as four per lane on an Illumina HiSeq 2000.

Vehicle 0.02% DMSO

PLEASE DO NOT EDIT THE COTENTS ABOVE