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Sample GSM1519641 Query DataSets for GSM1519641
Status Public on Nov 13, 2014
Title ChIP:MYB_ab45150_Jurkat3_091914 [lab: Look-DFCI]
Sample type SRA
 
Source name T-ALL
Organism Homo sapiens
Characteristics cell type: Jurkat
chip antibody: MYB
antibody manu.: Abcam
antibody catalog: ab45150
young_id: 20140924_3095
system: Blood
tal1 enhancer status: WT-11bp/Jurkat
Treatment protocol Untreated
Growth protocol Cells were grown according to ATCC guidelines
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 Images analysis and base calling was done using the solexa pipeline.
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
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 06, 2014
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
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 (1)
GSE59657 An Oncogenic Super-Enhancer Formed through Somatic Mutation of a Noncoding Intergenic Element
Relations
BioSample SAMN03097491
SRA SRX725584

Supplementary file Size Download File type/resource
GSM1519641_20140924_3095.974.rpm.WIG.gz 84.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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