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Sample GSM2359435 Query DataSets for GSM2359435
Status Public on Oct 23, 2017
Title 1_A375 DMSO_BRD4 [lab: Hammerman-DFCI]
Sample type SRA
Source name Melanoma
Organism Homo sapiens
Characteristics cell line: A375
chip antibody: Brd4
antibody manufacturer: Bethyl
antibody catalog number: A301-985A100
young_id: 20160603_4845
tissue: Skin
drug: DMSO
concentration: 0.1%
cell number: 50 million
treatment duration: 48h
Treatment protocol Cells were treated with DMSO for 48 hours prior to cross linking with formaldehyde.
Growth protocol A375 cells were grown in DMEM, 10% FBS, PSG at 37 degrees and 5% CO2. Cells were maintained between 40-90% confluency.
Extracted molecule genomic DNA
Extraction protocol 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.
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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Data processing Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
Submission date Oct 24, 2016
Last update date May 15, 2019
Contact name Richard A Young
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platform ID GPL16791
Series (2)
GSE89128 Suppression of adaptive responses to targeted cancer therapy by transcriptional repression [ChIP-seq]
GSE89129 Suppression of adaptive responses to targeted cancer therapy by transcriptional repression
BioSample SAMN05938355
SRA SRX2267438

Supplementary file Size Download File type/resource
GSM2359435_20160603_4845.7212.rpm.WIG.gz 72.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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