|
| Status |
Public on Feb 02, 2015 |
| Title |
MB_shKap1_RNAseq_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H
developmental stage: proliferating myoblasts
genotype/variation: LV sh-Kap1 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 |
SAMN03140304 |
| SRA |
SRX739772 |
