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. Author manuscript; available in PMC: 2022 Jun 30.
Published in final edited form as: Cell Rep. 2022 Jun 14;39(11):110944. doi: 10.1016/j.celrep.2022.110944

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit polyclonal anti-ERα Kraus and Kadonaga (1998) N/A
Rabbit polyclonal anti-ERα Millipore Sigma Cat. No. 06-935
RRID: AB_310305
Rabbit polyclonal anti-panSRC Acevedo et al. (2004) N/A
Rabbit polyclonal anti-ß-tubulin Abcam Cat. No. MABE1031
RRID: AB_2210370
Rabbit polyclonal anti-SNRNP70 Abcam Cat. No.: ab83306
RRID: AB_10673827
Mouse monoclonal anti-Flag Sigma-Aldrich Cat. No.: F3165
RRID: AB_259529
Rabbit polyclonal anti-Cas9 Diagenode Cat. No.: C15310258
RRID: AB_2715516
Rabbit polyclonal anti-H3K27ac Abcam Cat. No.: ab4729
RRID: AB_2118291
Mouse monoclonal anti-p300 Active Motif Cat. No.: 61401
RRID: AB_2716754
Rabbit polyclonal anti-H3 Abcam Cat. No.: ab1791
RRID: AB_302613
Rabbit polyclonal anti-BCAS2 Bethyl Cat. No.: A300-915A
RRID:AB_661883
Mouse monoclonal anti-BCAS2 Santa Cruz Cat. No.: sc-365346
RRID: AB_10846085
Goat anti-rabbit HRP-conjugated IgG ThermoFisher Cat. No. 31460
RRID: AB_228341
Goat anti-mouse HRP-conjugated IgG ThermoFisher Cat. No. 31430
RRID: AB_10960845
Rabbit IgG ThermoFisher Cat. No. 10500C
RRID: AB_2532981
Chemicals, peptides, and recombinant proteins
p300 Gupte et al. (2021) N/A
6xHis-BCAS2 This study N/A
Human H3.1/H4 tetramer NEB Cat. No.: M2509
17β-estradiol Sigma Cat. No.: E8875
Doxycycline Sigma Cat. No.: D9891
A485 Tocaris Cat. No.: 6387
Critical commercial assays
RNA ScreenTape Agilent Technologies Cat. No.: 5067-5576, 5067-5577
DNA ScreenTape Agilent Technologies Cat. No.: 5067-5584, 5067-5585
Deposited data
MCF-7 ±E2, ±TAP PRO-cap This study GEO: GSE175469
MCF-7 E2, polyA-depleted RNA-seq This study GEO: GSE175469
MCF-7 E2, polyA-enriched RNA-seq This study GEO: GSE175469
MCF-7, siCtrl, ±E2 RNA-seq This study GEO: GSE175469
MCF-7, siBCAS2 #1, ±E2 RNA-seq This study GEO: GSE175469
MCF-7, siBCAS2 #2, ±E2 RNA-seq This study GEO: GSE175469
MCF-7, siCtrl, ±E2, ERα ChIP-Seq This study GEO: GSE175469
MCF-7, siBCAS2 #1, ±E2, ERα ChIP-seq This study GEO: GSE175469
MCF-7, siCtrl, ±E2, Input ChIP-Seq This study GEO: GSE175469
MCF-7, siBCAS2 #1, ±E2, Input ChIP-seq This study GEO: GSE175469
PRRX2 WT eRNA Proteomics This study MassIVE: MSV000087492
PRRX2 MT eRNA Proteomics This study MassIVE: MSV000087492
PRRX2 GFP RNA Proteomics This study MassIVE: MSV000087492
FERM Proteomics This study MassIVE: MSV000087492
Experimental models: Cell lines
293T ATCC Cat. No.: CRL-3216
RRID: RRID:CVCL_0063
MCF-7 Dr. Benita Katzenellenbogen, University of Illinois, Urbana-Champaign
Oligonucleotides
Primers for molecular cloning See Table S2 N/A
Recombinant DNA
pLenti-dCas9-Flag-Blast This study N/A
pINDUCER20 Addgene Cat. No.: 44012
pIND20-sgRNA-eRNA-bGHpA This study N/A
pIND20-PRRX2(sgRNA)-bGHpA This study N/A
pIND20-PRRX2(eRNA)-bGHpA This study N/A
pIND20-PRRX2(sgRNA)-PRRX2(eRNA)-bGHpA This study N/A
pIND20-UBE2E2(sgRNA)-bGHpA This study N/A
pIND20-UBE2E2(eRNA)-bGHpA This study N/A
pIND20-UBE2E2(sgRNA)-UBE2E2(eRNA)-bGHpA This study N/A
pIND20-PRRX2(sgRNA)-UBE2E2(eRNA)-bGHpA This study N/A
pIND20-PRRX2(sgRNA)-SEMA3C(eRNA)-bGHpA This study N/A
pIND20-UBE2E2(sgRNA)-PRRX2(eRNA)-bGHpA This study N/A
pIND20-UBE2E2(sgRNA)-SEMA3C(eRNA)-bGHpA This study N/A
pIND20-P2RY2(sgRNA)-bGHpA This study N/A
pIND20-P2RY2(eRNA)-bGHpA This study N/A
pIND20-P2RY2(sgRNA)-P2RY2(eRNA)-bGHpA This study N/A
pIND20-SEMA3C(sgRNA)-bGHpA This study N/A
pIND20-SEMA3C(eRNA)-bGHpA This study N/A
pIND20-SEMA3C(sgRNA)-SEMA3C(eRNA)-bGHpA This study N/A
pIND20-PRRX2(sgRNA)-FERM-bGHpA This study N/A
pIND20-UBE2E2(sgRNA)-FERM-bGHpA This study N/A
pIND20-SEMA3C(sgRNA)-FERM-bGHpA This study N/A
pIND20-PRRX2(sgRNA)-PRRX2(ΔFERM eRNA)-bGHpA This study N/A
pIND20-UBE2E2(sgRNA)-UBE2E2(ΔFERM eRNA)-bGHpA This study N/A
pIND20-PRRX2(sgRNA)-PRRX2(MT eRNA)-bGHpA This study N/A
pIND20-PRRX2(sgRNA)-PRRX2(WT.AS eRNA)-bGHpA This study N/A
pcDNA3.1(+)-PRRX2(WT)eRNA This study N/A
pcDNA3.1(+)-PRRX2(MT)eRNA This study N/A
pcDNA3.1(+)-PRRX2(WT.AS)eRNA This study N/A
pcDNA3.1(+)-UBE2E2(eRNA) This study N/A
pcDNA3.1(+)-SEMA3C(eRNA) This study N/A
pcDNA3.1(+)-GFP This study N/A
pET19b-6xHis-BCAS2 This study N/A
pCMV-VSV-G Addgene Cat. No.: 8454
psPAX2 Addgene Cat. No.: 12260
PAdVAntage Promega Cat. No.: TB207
Software and algorithms
FastQC Babraham Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Star Dobin et al. (2013) https://github.com/alexdobin/
STAR
BWA Li and Durbin (2009) http://bio-bwa.sourceforge.net/
StringTie Pertea et al. (2016) https://ccb.jhu.edu/software/stringtie/
Cappable-seq Ettwiller et al. (2016) https://github.com/Ettwiller/TSS
BEDtools Quinlan and Hall, (2010) https://bedtools.readthedocs.io/en/latest/
SAMtools Li et al. (2009) http://www.htslib.org/
BEDops Neph et al. (2012) https://bedops.readthedocs.io/
Deeptools Ramirez et al. (2016) https://deeptools.readthedocs.io/en/develop/
SparK Kurtenbach and Harbour (2019) https://github.com/harbourlab/SparK
Subread Liao et al., (2013) http://subread.sourceforge.net/
DESeq2 Love et al. (2014) https://bioconductor.org/packages/release/bioc/html/DESeq2.html
MEME Suite Bailey et al. (2009) https://meme-suite.org/meme/index.html
DAVID Bioinformatics Resources Huang da et al. (2009) https://david.ncifcrf.gov/
RNAfold Lorenz et al., (2011) http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi
Scanfold Andrews et al. (2018) https://github.com/moss-lab/ScanFold
Proteome Discoverer ThermoFisher Cat. No.: OPTON-30812
msmsTests Gregori et al. (2020) https://www.bioconductor.org/packages/release/bioc/html/msmsTests.html