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Sample GSM1553135 Query DataSets for GSM1553135
Status Public on Jan 07, 2016
Sample type SRA
Source name SUM159R
Organism Homo sapiens
Characteristics cell line: SUM159R
chip antibody: none
drug treatment: DMSO
duration: 3 hour
barcode (already removed): CTTGTA
Treatment protocol Cells were treated with 500 nM JQ1 or DMSO for the indicated time
Growth protocol Cells were growed with SUM medium
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description ChIP-Seq whole cell extract input control from DMSO treated cells
Sample name: SUM159R_BRD4_DMSO_WCE_R1
Data processing Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format
Submission date Nov 24, 2014
Last update date May 15, 2019
Contact name Kornelia Polyak
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL18573
Series (2)
GSE63581 Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [ChIP-Seq]
GSE63584 Response and resistance to BET bromodomain inhibitors in triple negative breast cancer
BioSample SAMN03218097
SRA SRX795224

Supplementary file Size Download File type/resource
GSM1553135_SUM159R_BRD4_DMSO_WCE_R1.wig.gz 31.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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