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Sample GSM1545038 Query DataSets for GSM1545038
Status Public on Jan 07, 2016
Title SUM159_JQ1_CHEM_SEQ_R1
Sample type SRA
Source name SUM159
Organism Homo sapiens
Characteristics cell line: SUM159
sonicated nuclear lysates incubated with: Biotin-JQ1
dna fragments precipitated using: Streptavidin
barcode (already removed): GATCAG
Treatment protocol Sonicated nuclear lysates were incubated with Biotin-JQ1 for 6 hour
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 precipitated using streptavidin conjugated beads. Purified precipitated 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 OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Description Chem-Seq for Biotin JQ1
Data processing library strategy: Chem-Seq
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 14, 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)
GSE63284 Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [Chem-Seq]
GSE63584 Response and resistance to BET bromodomain inhibitors in triple negative breast cancer
BioSample SAMN03178262
SRA SRX836254

Supplementary file Size Download File type/resource
GSM1545038_SUM159_JQ1_CHEM_SEQ_R1.wig.gz 116.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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