 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 15, 2013 |
| Title |
Activated_SatCells_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Satellite Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H
developmental stage: satellite cells 72hrs in GM
chip antibody: none
|
| 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.
|
| Growth protocol |
C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Ribosome minus total RNA sequencing
|
| 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
Bigwig files were generated using BedTools (Quinlan AR and Hall IM, 2010) and wigToBigWig(UCSC genome browser website) programs
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; bigwig files
|
| |
|
| Submission date |
Aug 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hossein Zare |
| E-mail(s) |
hzare@mail.nih.gov
|
| Organization name |
NIH
|
| Street address |
5o South Dr #1347
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE49313 |
eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci |
|
| Relations |
| BioSample |
SAMN02318533 |
| SRA |
SRX335903 |
| Named Annotation |
GSM1210416_Activated_SatCells_RNA.bigwig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1210416_Activated_SatCells_RNA.bigwig |
736.6 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
