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Sample GSM3263343 Query DataSets for GSM3263343
Status Public on Jul 09, 2019
Title MDAMB231_BRD4_DMSO_48h_rDNA
Sample type SRA
Source name MDAMB231 breast carcinoma cell line
Organism Homo sapiens
Characteristics cell line: MDAMB231
treatment: DMSO 48h rDNA
culture media: DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone
library preparation kit: KAPA Hyper Prep
chip antibody: BRD4 Bethyl Laboratories A301-985A
Extracted molecule genomic DNA
Extraction protocol Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description MDAMB231_rDNA_250bp_bins.xlsx
Data processing Reads were aligned to hg19 or to a single copy of the ribosomal DNA repeat (GenBank: U13369.1) using Bowtie v1.1.2 with parameters -v 2 -m 1.
Genome_build: hg19
Supplementary_files_format_and_content: The following processing steps were performed to generate peakclassification files: Calculating read density: The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads (rpm). The read density of the input chromatin was subtracted from the ChIP read density for normalization. Peak calling: We used a combination of two algorithms, MACS v1.4.2 and HMCan v1.21, to define enriched regions. We used HMCan to call peaks in regions of high CNV, defined as regions of size > 50 kb where no MACS peaks are called, and have read coverage that is >3 times the average read coverage. Peaks within 12.5 kb of each other were stitched as described in Loven et al. 2013 Cell 153. We used default settings for MACS, and HMCan was run with narrow peak calling configuration file with no blacklisted regions. Peak genic classification: A peak region was classified on the basis of its location with respect to GRCh37/hg19 gene annotations. If the region was +/- 5 kb of any transcription start site, it was classified as a promoter peak. If it was within -5kb to -200kb of any transcriptional start site, it was classified as a 5' enhancer peak. If the peak overlapped the gene boundary, and was not classified as a promoter or enhancer peak, it was classified as either a genebody_exon or genebody_intron peak. If the peak resided within 0 to +200kb from the 3'-most exon, and did not fulfill the criteria for the above classifications, it was classified as a 3' enhancer. All remaining peaks were designated as "other".
Submission date Jul 10, 2018
Last update date Jul 09, 2019
Contact name Gary L Johnson
Phone 919-843-3107
Organization name UNC Chapel Hill SOM
Department Pharmacology
Lab Gary L. Johnson
Street address 120 Mason Farm Road Genetic Medicine Building CB#7365
City Chapel Hill
State/province North Carolina
ZIP/Postal code 27599
Country USA
Platform ID GPL18573
Series (2)
GSE116879 Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination (ChIPseq)
GSE116919 Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination
BioSample SAMN09638165
SRA SRX4377555

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

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