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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 23, 2011 |
| Title |
CTL_Flavo_PolII_8W |
| Sample type |
SRA |
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| Source name |
C2C12 myoblasts
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| Organism |
Mus musculus |
| Characteristics |
strain: C3H
cell line: C2C12 myoblasts
agent: control
chip antibody: PolII 8WG16
chip antibody vendor: Covance
chip antibody lot#: E10015AF
chip antibody catalog#: MMS-126R
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| Treatment protocol |
Control sample: These were C2C12 cells which were placed in differentiation media (DMEM + 2% horse serum + insulin-transferrin-seleniumG) for 6hrs.
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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 IIx |
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| Description |
Chromatin IP against PolII (Control treatment)
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| Data processing |
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 |
Oct 21, 2011 |
| 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 |
GPL11002 |
| Series (1) |
| GSE25549 |
Polycomb Protein Ezh1 Promotes RNA Polymerase II Elongation |
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| Relations |
| SRA |
SRX101682 |
| BioSample |
SAMN00739950 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM820617_CTL_Flavo_PolII_8W.bed.gz |
100.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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