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Sample GSM2586705 Query DataSets for GSM2586705
Status Public on Mar 20, 2019
Title mock_BRD4_A
Sample type SRA
Source name Cell Line
Organism Homo sapiens
Characteristics tissue: prostate
cell type: prostate cancer cell line
Treatment protocol DMSO was diluted 1:2000 to 0.05% in appropriate cell culture media. Serves as vehicle control for JQ1 treatment. Samples for ChIP-seq were treated for 12 hours.
Growth protocol PC3 cells were grown in RPMI1640 + 10% FBS (Premium Select grade, Atlanta Biologicals).
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were performed with formaldehyde cross-linked cells using anti-BRD4 antibody (Bethyl #A301-985A). Input and ChIP samples were processed using Diagenode iDeal ChIP-seq for Transcription Factors Kit.
Illumina TruSeq ChIP Sample Prep Kit, using 10 ng of input material.
RNA: Trizol/CHCl3; ChIP: formaldedhyde cross-linking followed by Diagenode iDeal ChIP-seq for Transcription Factors Kit. Also see SAMPLES section.
RNA-seq: Agilent SureSelect Strand-Specific mRNA Library Preparation Protocol; ChIP-seq: Illumina TruSeq ChIP Sample Prep Kit. Also see SAMPLES section.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Sequences in raw .fastq files trimmed to 100bp.
Confirmed sequencing quality with FastQC utility.
Aligned .fastq files using bwa utility witn bwa-mem algorithm.
Converted to sorted .bam files ising samtools view and samtools sort utilities
Sequencing quality further confirmed using samtools stats utility.
For later analysis, translated out output .bam to sorted .bed files using bedtools utility.
Called peaks using epic peak caller.
Genome_build: hg38 release 85
Supplementary_files_format_and_content: .bed (called ChIP-seq peaks)
Supplementary_files_format_and_content: counts
Submission date Apr 21, 2017
Last update date May 15, 2019
Contact name Joshi Alumkal
Organization name Knight Cancer Institute
Street address 3303 SW Bond Ave. CH14R
City Portland
State/province OR
ZIP/Postal code 97239
Country USA
Platform ID GPL11154
Series (1)
GSE98069 BET Bromodomain Inhibition Blocks the Function of a Critical AR-Independent Master Regulator Network in Lethal Prostate Cancer
BioSample SAMN06812533
SRA SRX2752495

Supplementary file Size Download File type/resource
GSM2586705_mock_BRD4_A-coverage-summary.bed.gz 1.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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