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. Author manuscript; available in PMC: 2021 Nov 3.
Published in final edited form as: Cell Rep. 2020 Jun 23;31(12):107803. doi: 10.1016/j.celrep.2020.107803

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit polyclonal anti-ERα Bethyl A300-495A; RRID: AB_451030
Rabbit polyclonal anti-RNA Polymerase II Santa Cruz Biotechnology SC-9001; RRID: AB_2268548
Mouse monoclonal anti-RNA Polymerase II Santa Cruz Biotechnology SC-56767; RRID: AB_785522
Mouse monoclonal anti-RNA Polymerase II Abcam ab817; RRID: AB_306327
Rabbit polyclonal anti-KDM2A Proteintech 24311-1-AP
Rabbit monoclonal anti-NEDD4 Cell Signaling Technology 3607; RRID: AB_2149311
Mouse monoclonal anti-GST tag Proteintech 66001-2
Mouse monoclonal anti-His tag Proteintech 66005-1; RRID: AB_11232599
Mouse monoclonal anti-Lamin A/C Abcam ab8984; RRID: AB_306913
Mouse monoclonal anti-GAPDH Santa Cruz Biotechnology SC-365062; RRID: AB_10847862
Rabbit polyclonal anti-RAD21 Abcam ab992; RRID: AB_2176601
Mouse monoclonal anti-FLAG Sigma F1804; RRID: AB_262044
Bacterial and Virus Strains
Rosetta 2(DE3) Singles ™ Competent Cells Emdmillipore 71400-3
Chemicals, Peptides, and Recombinant Proteins
17β-estradiol Sigma E2758
fulvestrant Medchem Express HY13636
4-Thiouridine Sigma T4509
RNase A/T Thermo Fisher EN0551
RNase Cocktail™ Enzyme Mix Thermo Fisher AM2286
SYBR Green Supermix BioRad 1725124
GST-KDM2A Abcam ab151923
Critical Commercial Assays
Dual-Luciferase reporter assay kit Promega E1910
ThruPLEX DNA-seq kit Rubicon R400427
Q5 Site-Directed Mutagenesis kit NEB E0554S
Deposited Data
Raw and processed sequencing data This paper GEO: GSE135341
Experimental Models: Cell Lines
MCF-7 ATCC HTB-22
ZR-75-1 ATCC CRL-1500
MCF-7 with BLRP-ERα-wild type Liu et al., 2014 GSE135341
MCF-7 with BLRP-P-Box mutant Liu et al., 2014 GSE135341
Oligonucleotides
siRNAs targeting eRNAs: see Table S1 This paper N/A
LNAs targeting eRNAs: see Table S1 This paper N/A
Primers for detecting mRNAs by RT-qPCR: see Table S2 This paper N/A
Primers for detecting eRNAs by RT-qPCR: see Table S2 This paper N/A
Primers for targeted ChIP-qPCR: see Table S4 This paper N/A
Primers for 3C: see Table S3 This paper N/A
Recombinant DNA
pGEX-ERα-fragments Zhang et al., 2013 N/A
pCDH-EF1-MCS-T2A Systembioscience CD527A-1
pGL3 Li et al., 2013 N/A
pET28a(+) EMD Biosciences 69864-3
Software and Algorithms
STAR v2.5.2b Dobin et al., 2013; Theodorou et al., 2013 https://github.com/alexdobin/STAR
featureCounts v1.5.1 Liao et al., 2014 http://subread.sourceforge.net/
DESeq2 v1.14.1 Love et al., 2014 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Bowtie v1.1.2 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml
MACS2 v2.1.1.20160309 Zhang et al., 2008 https://github.com/taoliu/MACS
HOMER v4.8 Heinz et al., 2010 http://homer.ucsd.edu/homer/index.html
edgeR v3.16.5 Robinson et al., 2010 https://bioconductor.org/packages/release/bioc/html/edgeR.html
Other
H3K27ac ChIP-Seq data Li et al., 2013 GEO: GSE45822
H3K4me1 ChIP-Seq data Theodorou et al., 2013 GEO: GSE40129
DHS-Seq data He et al., 2012 GEO: GSE33216
FOXA1 ChIP-Seq data Kong et al., 2011 GEO: GSE26831
RNA Pol II ChIP-Seq data Li et al., 2013 GEO: GSE45822
ERα ChIP-Seq data 1 Schmidt et al., 2010 ArrayExpress: E-TABM-828
ERα ChIP-Seq data 2 Tsai et al., 2010b GEO: GSE24166
CTCF, STAG1 and RAD21 ChIP-Seq data Schmidt et al., 2010 ArrayExpress: E-TABM-828
Time course ERα ChIP-Seq data 1 GEO: GSE94023
Time course ERα ChIP-Seq data 2 Honkela et al., 2015 GEO: GSE62789
GRO-Seq data 1 Li et al., 2013 GEO: GSE45822
GRO-Seq data 2 Franco et al., 2015 GEO: GSE59532
RNA Pol II ChIA-PET data Li et al., 2012; Natoli and Andrau, 2012 GEO: GSE33664
CTCF ChIA-PET data ENCODE Project Consortium, 2012 GEO: GSE39495