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Sample GSM808748 Query DataSets for GSM808748
Status Public on Oct 06, 2011
Title PolII_ChIPSeq_rep1
Sample type SRA
 
Source name primary myotubes
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: myotubes induced from wild type mouse fetal (E18.5) primary myoblasts
passages: 17
chip antibody: Pol II
antibody vender: Abcam
antibody lot/batch#: no record
antibody catalog#: ab5408
Growth protocol Primary myoblasts isolated from wild type mouse fetal (E18.5) limb muscle were cultured in differentiation medium (DMEM + 2% horse serum) for 48 hours to induce myotubes.
Extracted molecule genomic DNA
Extraction protocol DNA Imprint Chromatin Immunoprecipitation Kit (vender: Sigma-Aldrich) includes all necessary reagents for isolating genomic DNA in addition to those for ChIP. Immunoprecipitated Immunoprecipitated material was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18-cycles of PCR and size selected (300-600 bp) followed by single end sequencing on an Illumina Genome Analyzer II.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Chromatin IP against Pol II
Data processing Alignment: Sequence reads were obtained and mapped to the mouse (NCBI37/mm9) genome using Bowtie (version 0.12.5) (http://bowtie-bio.sourceforge.net/index.shtml). All reads mapping with two or fewer mismatches were retained.
Peaks: Peak calling was performed with SISSRs (version 1.4) (http://sissrs.rajajothi.com/)
 
Submission date Oct 05, 2011
Last update date May 15, 2019
Contact name Chung-Il An
Organization name University of California, Davis
Street address One Shields Ave.
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL9250
Series (1)
GSE32627 Genome-wide mapping of Sox6 binding sites in mouse fetal myotubes
Relations
SRA SRX099707
BioSample SAMN00736187

Supplementary file Size Download File type/resource
GSM808748_Pol2_1.bed.gz 23.2 Mb (ftp)(http) BED
GSM808748_Pol2peak_1.gff.gz 135.9 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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