|
| Status |
Public on Apr 30, 2014 |
| Title |
RNASeq-dMes4-KD2- S2 Cells |
| Sample type |
SRA |
| |
|
| Source name |
Late embryonic derived S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 Schneider cells
|
| Treatment protocol |
S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for beaf32 or luc were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 5 days and cells were then harvested.
|
| Growth protocol |
S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/ (GIBCO, Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were purified into Trizol.
Libraries were prepared by the MGX platform (http://mgx-project.igf.cnrs.fr) for Digital Gene expression by Tag-sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA extraction in trizol
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Burrows Wheeler Alignment tool (BWA) software (default parameters) was used for base-calling
DEGSeq package (Wang et al., 2010) was then used to identify differentially expressed genes (p-value<0.001)
Genome_build: Flybase release 5.41
Supplementary_files_format_and_content: tab-delimited text files
|
| |
|
| Submission date |
Apr 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Olivier Cuvier |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS
|
| Department |
LBME
|
| Lab |
Chromatin Dynamics & Cell proliferation
|
| Street address |
118 route de Narbonne
|
| City |
Toulouse |
| ZIP/Postal code |
31062 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE57167 |
Illumina Sequencing data of the influence on gene expression of insulator protein co-factor dMes-4 |
| GSE57168 |
Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes |
|
| Relations |
| BioSample |
SAMN02740911 |
| SRA |
SRX529176 |
