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Status |
Public on Nov 23, 2011 |
Title |
MT_H3K27me3_ChIPSeq |
Sample type |
SRA |
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Source name |
C2C12 myoblasts
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Organism |
Mus musculus |
Characteristics |
strain: C3H developmental stage: 48-hours differentiated Myotubes chip antibody (epitope/name): H3K27me3 chip antibody details (vendor/catalog #): Millipore/17-622
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Treatment protocol |
For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.
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Growth protocol |
C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin.
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Extracted molecule |
genomic DNA |
Extraction protocol |
For ChIPSeq, cells were cross-linked in 1% formaldehyde and processed according to Lee, T. I., Johnstone, S. E. & Young, R. A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748 (2006). bfChIP were performed according to Kim, J., Chu, J., Shen, X., Wang, J. & Orkin, S. H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049-1061 (2008). Purified DNA was processed according to manufacturer's protocol. For mRNASeq, Illumina protocol was followed.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer II |
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Description |
Chromatin IP against H3K27me3 MT_H3K27me3.fq.tar.gz
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Data processing |
Instrument model: Illumina Genome Analyzer Iix ChIPSeq data were mapped to the mouse genome (mm9 version) using ELAND algorithm integrated within Illumina parallel sequencing analyzer software. For mRNA-Seq, TOPHAT package was used to map the reads to the genome and spliced junctions, Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
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Submission date |
Nov 22, 2010 |
Last update date |
May 15, 2019 |
Contact name |
Kambiz Mousavi |
E-mail(s) |
mousavik@mail.nih.gov
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Phone |
301-435-5648
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Fax |
301-480-9699
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Organization name |
National Institutes of Health
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Department |
National Institute of Arthritis and Musculoskeletal and Skin Diseases
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Lab |
Laboratory of Muscle Stem Cells and Gene Regulation
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Street address |
50 South Drive, Room 1347
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City |
Bethesda |
State/province |
MD |
ZIP/Postal code |
20892-8024 |
Country |
USA |
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Platform ID |
GPL9250 |
Series (1) |
GSE25549 |
Polycomb Protein Ezh1 Promotes RNA Polymerase II Elongation |
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Relations |
SRA |
SRX031887 |
BioSample |
SAMN00138473 |
Supplementary file |
Size |
Download |
File type/resource |
GSM628008_MT_H3K27me3.txt.gz |
332.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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