|
| Status |
Public on May 15, 2012 |
| Title |
S2_DMSO_Control |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: cultured cells of embryonic origin
cell line: S2
agent: DMSO
time point: 0min
|
| Treatment protocol |
Inhibitor added to the medium of growing cells for defined times
|
| Growth protocol |
Schneider medium (Gibco) at 25 degrees celsius
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exponentially growing Drosophila S2 cells were treated with either DMSO or Hsp90 inhibitor radicicol dissolved in DMSO at 40 micromolar concentration. The treatment was carried out for indicated periods of time after which cells were harvested, and RNA extracted using TRIzol (invitrogen). Poly(A) RNA were processed for sequencing using Illumina TruSeq manual.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
The number of reads mapping into ensembl genes models were counted using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) for subsequent differential expression analysis. Reads were aligned using Bowtie with the following parameter setting: --best --chunkmbs 512 -S -M 100 -p 8 -k 1. Unspecified parameters were set to default values. The dm3 BDGP Release5 was used as reference.
|
| |
|
| Submission date |
Feb 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Cem Sievers |
| E-mail(s) |
cem.sievers@bsse.ethz.ch
|
| Organization name |
ETH Zurich
|
| Street address |
Mattenstrasse
|
| City |
Basel |
| ZIP/Postal code |
4057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE35812 |
Radicicol treatment of Drosophila cells |
|
| Relations |
| Reanalyzed by |
GSM3276596 |
| SRA |
SRX120036 |
| BioSample |
SAMN00790439 |
