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Sample GSM1531001 Query DataSets for GSM1531001
Status Public on Feb 02, 2015
Title MT_shCtrl_RNAseq
Sample type SRA
 
Source name C2C12 myoblasts
Organism Mus musculus
Characteristics strain: C3H
developmental stage: 48-hours differentiating myoblasts
genotype/variation: LV sh-Luc transduced
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 calf serum (FCS) and penicillin/streptomycin.
Extracted molecule polyA RNA
Extraction protocol cytoplasmic RNA was extracted with Qiagen miRNeasy kit + on column DNAse treatment. The quality was assessed on a bioanalyzer, analyzed by RT-qPCR with positive and negative controls, selected for polyA+ RNA and sequenced.
Libraries were prepared according to Illumina's instructions
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Raw reads were mapped to the human genome (mm9) using Tophat 2.0.11 without asking for novel novel junctions nor indels in sensitive mode
Count per gene were obtained with htseq-count
Genome_build: mm9
Supplementary_files_format_and_content: csv containing the raw counts table with rows as genes and columns as samples.
 
Submission date Oct 23, 2014
Last update date May 15, 2019
Contact name Evarist Planet
E-mail(s) [email protected]
Organization name EPFL
Lab LVG
Street address Route Cantonale
City Lausanne
State/province Vaud
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL13112
Series (2)
GSE62659 A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation (RNA-seq)
GSE62664 A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation
Relations
Reanalyzed by GSE80797
BioSample SAMN03140306
SRA SRX739767

Supplementary file Size Download File type/resource
GSM1531001_mm9_MTshE_old.pileup.txt.gz 148.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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