|Public on Dec 07, 2017
|bladder cancer cells
|cell type: JMSU-1
chip antibody: H3K27Ac (Abcam, 4729, lot GR286678-2)
genotype: RXRA WT
|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.
|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).
|Illumina HiSeq 3000
|Base calls performed on the HiSeq 3000 run with RTA 2.7.3 and the HiSeq 2500 run was processed with RTA 220.127.116.11
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.
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
|Dec 05, 2017
|Last update date
|May 15, 2019
|Vivek K Arora
|Washington University School of Medicine
|660 S Euclid Ave
|Bladder Cancer Associated Mutations in RXRA activate Peroxisome Proliferator-Activated Receptors to Drive Urothelial Proliferation
|Bladder cancer associated mutations in RXRA activate peroxisome proliferator-activated receptors