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| Status |
Public on Sep 15, 2013 |
| Title |
MB_MyoD_ChIPseq |
| Sample type |
SRA |
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| Source name |
C2C12
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| Organism |
Mus musculus |
| Characteristics |
strain: C3H
developmental stage: Proliferating Myoblasts
chip antibody: MyoD (C-20, Santa Cruz)
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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 bovine serum (FBS) and penicillin/streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNA-Seq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and processed according to Mousavi et al. 2012. Purified DNA was processed according to manufacturer's protocol. For polyA RNA-Seq, Illumina protocol was followed. For ribosomal depletion, ribo-zero was used (epicenter).
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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 MyoD
MB_MyoD_ChIPseq1
MB_MyoD_ChIPseq2
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using illumina pipline (Eland) , and TopHat(Trapnell C, et.al 2009) for RNA-Seq
MyoD and MyoG Peaks were called using MACS ( Zhang et al, 2008), with pvalue of 10^-6, --gsize mm, and the rest were default setting. H3k4me1 peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: peak files in bed formats and wig files were generated using filtered reads residing in enriched regions
Supplementary_files_format_and_content: RNA-Seq: txt files represent FPKM(RPKM) and differential expression analysis
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| Submission date |
Jul 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hossein Zare |
| E-mail(s) |
hzare@mail.nih.gov
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| Organization name |
NIH
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| Street address |
5o South Dr #1347
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| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE49313 |
eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci |
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| Relations |
| BioSample |
SAMN02296793 |
| SRA |
SRX328690 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1197184_MB_Myod.wig.gz |
3.7 Mb |
(ftp)(http) |
WIG |
| GSM1197184_MB_Myod_peaks.bed.gz |
264.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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