|
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 |