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Sample GSM2877300 Query DataSets for GSM2877300
Status Public on Dec 07, 2017
Title H3K27Ac_S427F_Rep2
Sample type SRA
 
Source name bladder cancer cells
Organism Homo sapiens
Characteristics cell type: JMSU-1
chip antibody: H3K27Ac (Abcam, 4729, lot GR286678-2)
genotype: RXRA S427F
Growth protocol JMSU-1 cells stably expressing RXRAwt or RXRAS427F were seeded in biological triplicate in 150 mm TC-treated culture dish and collected when 70-90% confluency was reached.
Extracted molecule genomic DNA
Extraction protocol Crosslinking and ChIP were performed as described for adherent cells in the ENCODE experiment summary for ENCSR000BJW (https://www.encodeproject.org/experiments/ENCSR000BJW/) .
Chromatin was sonicated using the Diagenode Pico Bioruptor. DNA-protein complexes were precipitated with antibodies against RXRA (PP-K8508-00 R&D Systems) and H3K27Ac (ab4729 Abcam).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Description H3K27Ac_S427F_Rep1_pooled_peaks-sorted-optimum.narrowPeak
Data processing Base calls performed on the HiSeq 3000 run with RTA 2.7.3 and the HiSeq 2500 run was processed with RTA 1.18.66.3
ChIP-seq reads were aligned to hg19 using NovoAlign version 3.04.06 with the command: novoalign -r None -l 30 -e 100 -i 230 140 –H
ChIP peaks for each condition were called using the IDR methodology with MACS version 2.1.1 as the peakcaller: macs2 callpeak --pvalue 1e-2 --to-large. The output of this
For each genotype the IDR peaks of RXRA were intersected with the IDR peaks of H3K27Ac using bedtools intersect. These intersected regions were used as the peak lists to run DiffBind on the H3K27Ac alignments.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files contain peaks called by the IDR pipeline as being reproducible between biological replicates for each genotype and factor combination
Supplementary_files_format_and_content: broadPeak file contains regions called by DiffBind to be differentially bound between H3K27Ac mutant versus H3k27Ac wild type at a FDR cutoff of 0.1. The signalValue column is the log2 fold change of mutant over wild type
 
Submission date Dec 05, 2017
Last update date May 15, 2019
Contact name Vivek K Arora
E-mail(s) arorav@wustl.edu
Organization name Washington University School of Medicine
Street address 660 S Euclid Ave
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL21290
Series (2)
GSE107734 Bladder Cancer Associated Mutations in RXRA activate Peroxisome Proliferator-Activated Receptors to Drive Urothelial Proliferation
GSE107783 Bladder cancer associated mutations in RXRA activate peroxisome proliferator-activated receptors
Relations
BioSample SAMN08138338
SRA SRX3450324

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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