Journal: Cell systems

Article Title: Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers

doi: 10.1016/j.cels.2017.08.011

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: DATA AND SOFTWARE AVAILABILITY Software: See Key Resources Table. table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies H3K27ac rabbit polyclonal Active Motif Cat# 39133; RRID:AB_2561016 H3K9me3 rabbit polyclonal Abcam Cat# ab8898; RRID:AB_306848 FLAG mouse monoclonal Sigma-Aldrich Cat# F1804; RRID:AB_262044 RNA pol II 4H8 mouse monoclonal Abcam Cat# ab5408; RRID:AB_304868 ER alpha rabbit polyclonal Santa Cruz Cat#sc-544; RRID:AB_631469 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins β-estradiol Sigma-Aldrich Cat# E2758 Trichostatin A Cayman Chemicals Cat# 89730; CAS 58880-19-6 Critical Commercial Assays ZR 96-well Quick-RNA Zymo Research Cat# R1053 KAPA Stranded mRNA-seq KAPA Biosystems Cat# KK8420 Power SYBR® Green RNA-to-CT™ 1-Step Applied Biosystems Cat# 4389986 Deposited Data Raw and analyzed ChIP-seq data This study {"type":"entrez-geo","attrs":{"text":"GSE99906","term_id":"99906"}} GSE99906 Raw and analyzed RNA-seq data This study {"type":"entrez-geo","attrs":{"text":"GSE99906","term_id":"99906"}} GSE99906 Experimental Models: Cell Lines Human: Ishikawa cells ECACC ECACC Cat# 99040201, RRID:CVCL_2529 Experimental Models: Organisms/Strains Ishikawa SID4x-dCas9-KRAB This study Oligonucleotides gBlocks, see Table S1 Primers for constructing and verifying dCas9 fusions and guide RNAs, see Table S2 Guide RNA targets, see Table S3 qPCR primers, see Table S4 Primers for sequencing ERBS deletions, see Table S5 Recombinant DNA dCas9-VP160 Cheng et al., 2013 Addgene 48227 pGL3-U6-PGK-Puro Shen et al., 2014 Addgene 51133 gRNA_cloningVector Mali et al., 2013 Addgene 41824 Software and Algorithms Bowtie Langmead et al., 2009 DOI: 10.1186/gb-2009-10-3-r25 MACS2 Zhang et al., 2008 DOI: 10.1186/gb-2008-9-9-r137 DESeq2 Love et al., 2014 DOI: 10.1186/s13059-014-0550-8 HISAT Kim et al., 2015 DOI: 10.1038/nmeth.3317 HTSeq Anders et al., 2015 DOI: 10.1093/bioinformatics/btu638 Bedtools Quinlan and Hall, 2010 DOI: 10.1093/bioinformatics/btq033 Prism 6 http://www.graphpad.com/scientific-software/prism/ Other Open in a separate window KEY RESOURCES TABLE Data produced in this study are available from GEO ( {"type":"entrez-geo","attrs":{"text":"GSE99906","term_id":"99906"}} GSE99906 ).

Techniques: Recombinant, SYBR Green Assay, Sequencing, Software