|
| Status |
Public on Aug 30, 2018 |
| Title |
MDAMB231_BRD4_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: Mammary gland adenocarcarcinoma epithelial cells derived from metastatic site
cell source: ATCC #HTB-26
modifications: Parental cells
chip antibody: Bethyl Laboratories # A301-985A100
|
| Growth protocol |
MDA-MB-231 were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of DMEM that was supplemented with 10% FBS, 1x penicillin/streptomycin, and 1x glutamax.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were grown to 80% confluence on 150cm plates and processed using the High Sensitivity ChIP-IT Kit (Active Motif cat #53040).
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ data were processed with Trimmomatic v0.32 to remove adapters and low-quality reads.
ChIP-seq reads were aligned to the hg19 human genome using BWA v0.7.13-r1126 with the following parameters: aln -q 5 -l 32 -k 2. RNA-seq reads were aligned to the hg19 human genome using STAR aligner (version 2.5.3a) with default parameters and RSEM (version 1.2.31) to obtain expected gene counts against the human RefSeq (release 76). ATAC-seq reads were aligned to the hg19 human genome using Bowtie2 v2.2.6.
Duplicate reads were removed using Picard tools (version 1.126 - http://broadinstitute.github.io/picard).
RNA-seq differential expression was determined using DESeq2 and R (version 3.2.3) with q-value <0.05.
ChIP-seq peaks were called using MACS2.1 with default parameters and –shiftsize 160 –nomodel –p 0.01 for all data except RING1B in human iPSCs. For all H3k27me3 and H2AK119ub1 data, we added the option –broad. Whole-cell extract input from the corresponding cell line were used as control. ATAC-seq peaks were called using the MACS2.1 with the parameters: -g hs -p 0.01 --nomodel --shift -75 --extsize 150 and a cutoff of q-value <0.05.
Homer annotatePeaks v4.8.3 was used for peak annotation.
Bedtools v2.26.0 intersect was used to determine peak overlaps.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain the indexed tag chromosome coordinates and score produced from MACS2 peak calling.
|
| |
|
| Submission date |
Nov 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ho Lam Chan |
| E-mail(s) |
hlchan@med.miami.edu
|
| Organization name |
University of Miami
|
| Department |
Human Genetics
|
| Lab |
Lluis Morey
|
| Street address |
1501 NW 10th Ave. BRB 742A
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE107176 |
Polycomb complexes associate with enhancers to promote oncogenic transcriptional programs in cancer |
|
| Relations |
| BioSample |
SAMN08045368 |
| SRA |
SRX3410386 |
