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Sample GSM1082348 Query DataSets for GSM1082348
Status Public on Feb 13, 2013
Title C2C12 WCE
Sample type SRA
Source name myotubes
Organism Mus musculus
Characteristics chip antibody: None
antibody vendor and catalog number: None WCE
Growth protocol C2C12 myoblasts were grown under typical C2C12 myoblast conditions. Myotube formation was induced for 48 hours in 2% horse serum and 1x selenium, transferrin and insulin.
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. Half of the cell lysate was used for immunoprecipitation. The chromatin extracts containing DNA fragments with an average size of 500 bp 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 Genome Analyzer II
Description WCE for C2C12 myotubes
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 GPL9250
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 SRX236484
BioSample SAMN01920472

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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