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Sample GSM1689151 Query DataSets for GSM1689151
Status Public on May 28, 2015
Title Jurkat_CTCF_input
Sample type SRA
Source name T-ALL
Organism Homo sapiens
Characteristics cell type: Jurkat
chip antibody: None
antibody manu.: NULL
antibody catalog: WCE
antibody lot: --
young_id: 20150124_3462
Growth protocol Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 10 min.
Extracted molecule genomic DNA
Extraction protocol 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.
Whole cell extracts were sonicated to solubilize the chromatin.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description 20150124_3462
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 May 18, 2015
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 GPL11154
Series (2)
GSE68976 Activation of proto-oncogenes by disruption of chromosome neighborhoods [ChIP-Seq]
GSE68978 Activation of proto-oncogenes by disruption of chromosome neighborhoods
BioSample SAMN03700051
SRA SRX1030323

Supplementary file Size Download File type/resource
GSM1689151_20150124_3462.2846.rpm.WIG.gz 92.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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