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Sample GSM1910996 Query DataSets for GSM1910996
Status Public on Oct 20, 2015
Title HEK293_Input
Sample type SRA
Source name Embryonic Kidney (HEK)
Organism Homo sapiens
Characteristics cell type: HEK293T
chip antibody: Input
antibody manu.: Input
antibody catalog: none
young_id: 20150925_4267
Growth protocol H293T cells were cultured in DMEM + 10% serum at 37°C / 5% CO2
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 HiSeq 2000
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 19, 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 SAMN04194064
SRA SRX1353401

Supplementary file Size Download File type/resource
GSM1910996_20150925_4267.6384.rpm.WIG.gz 53.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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