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Sample GSM1082342 Query DataSets for GSM1082342
Status Public on Feb 13, 2013
Title ChIP-Seq_Nanog_V65
Sample type SRA
Source name Embryonic stem cells
Organism Mus musculus
Characteristics chip antibody: Nanog
antibody vendor and catalog number: Bethyl A300-397A
background strain: C57BL/6-129
Growth protocol V6.5 embryonic stem cells V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.
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
Description Chromatin IP against NANOG in v6.5
Data processing Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 1 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended by MACS and allocated into 50bp bins
Submission date Feb 12, 2013
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 GPL13112
Series (2)
GSE44286 Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes [ChIP-Seq]
GSE44288 Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
SRA SRX236478
BioSample SAMN01920466

Supplementary file Size Download File type/resource
GSM1082342_10192012_C1AVNACXX_2.GTTTCG.wig.gz 52.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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