|
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 |