|
| Status |
Public on Jan 24, 2018 |
| Title |
RNAseq in AtT-20 expressing ER-Pax7 (24 hours) replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
AtT-20 cells expressing 3x flag-ER-Pax7
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pituitary corticotroph cell
passages: 10-20
cell line: AtT-20 cells
treatment: 24 hours of 4-hydroxy-Tamoxifen
mrna enrichment protocol: Ribosomal depletion
|
| Growth protocol |
AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We extracted total RNA using the Qiagen Rneasy kit and then performed ribosomal depletion on the extracted RNA
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA_ERPax7_ribo_count_gene_EdgeR.txt
|
| Data processing |
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed to obtain high quality reads and then mapped to the GRCm38 mouse genome build using TopHat
gene expression FPKM was determined using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: Differential gene expression analysis was performed with EdgeR
|
| |
|
| Submission date |
Sep 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
ALEXANDRE MAYRAN |
| E-mail(s) |
alexandre.mayran@epfl.ch
|
| Organization name |
EPFL
|
| Street address |
Station 19
|
| City |
LAUSANNE |
| State/province |
Waadt |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE87181 |
RNAseq in Pax7-reprogrammed corticotropes AtT-20 cells |
| GSE87185 |
Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate |
|
| Relations |
| BioSample |
SAMN05799359 |
| SRA |
SRX2182994 |
