|
| Status |
Public on Oct 20, 2010 |
| Title |
S2_eIF4AIII-1 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cell culture, eIF4AIII dsRNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2
treatment: eIF4AIII dsRNA
treatment time: 6 days
|
| Treatment protocol |
S2 cells were treated with dsRNAs (15ug/ml) corresponding to either GFP, eF4AIII or MAGO for six days.
|
| Growth protocol |
S2 cells were grown in Schneider Medium (Invitrogen) with 10% FBS and with Pen/Strep at 18C degrees.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from S2 cells subjected to treatment with eIF4AIII, mago and GFP dsRNA in duplicate was prepared using TRIzol reagent (Invitrogen). Poly(A)+ mRNAs were enriched using oligo(dT) selection with the Oligotex mRNA Midi kit (Qiagen). The resulting mRNA was then depleted of rRNA molecules using the Ribominus Eukaryote kit (Invitrogen). High-throughput sequencing libraries were prepared according to the SOLiD whole transcriptome library preparation protocol (Applied Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
Transcriptome of S2 cells treated with eIF4AIII dsRNA; replicate 1.
|
| Data processing |
Reads were mapped using ABI Bioscope 1.0.1 to both the Drosophila melanogaster genome (UCSC dm6) and a set of filter sequences, comprised of ribosomal and transfer RNA and sequencing adapters. Filtered reads are not removed from the results but simply marked as such. Both .bam and .wig files were generated using the Whole Transcriptome pipeline described in the ABI documentation. A read was considered unique even if other matches existed of length 3 less than the best match (clear zone = 3). The .wig file was generated using the default values for the sam2wig run (alignment score of 24 or higher and minimum coverage of 10).
|
| |
|
| Submission date |
Sep 18, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Hugo Lavoie |
| E-mail(s) |
hugo.lavoie@nrc-cnrc.gc.ca
|
| Phone |
514-496-6154
|
| Fax |
514-496-6213
|
| Organization name |
CNRC-IRB
|
| Department |
Genetics
|
| Street address |
6100 Royalmount
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4P 2R2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL10942 |
| Series (1) |
| GSE24012 |
Transcriptional profiling of EJC depletion by RNA-Seq using the SOLiD platform (Applied Biosystems) |
|
| Relations |
| SRA |
SRX035190 |
| BioSample |
SAMN00188796 |
