|
| 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 |
|
| Relations |
| BioSample |
SAMN06812533 |
| SRA |
SRX2752495 |
