|
| Status |
Public on Dec 07, 2017 |
| Title |
RXRA_S427F_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
bladder cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: JMSU-1
chip antibody: RXRA (Perseus Proteomics, K8508, lot A2)
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 |
RXRA_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 |
SAMN08138331 |
| SRA |
SRX3450331 |
