|
| Status |
Public on Dec 22, 2011 |
| Title |
Control RNA-Seq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Schneider's Drosophila Line 2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2; Schneider's Drosophila Line 2; Marco Blanchette's Lab
cell line: S2
knockdown: control
|
| Treatment protocol |
Drosophila RNAi was performed by feeding S2 cells with dsRNA prepared with the Megascript T7 dsRNA synthesis kit from Ambion (catalog #1626.) Cells at a density of 2e6 cells/ml were serum starved treated with 10 µg of dsRNA. Additional boosts of 10 µg dsRNA were added at 48 and 96 hours. Cells were harvested at 120 hours.
|
| Growth protocol |
S2 cells were grown in Schneider's media with 10% FBS at room temperature.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two micrograms of DNase-treated total RNA was depleted of Ribosomal RNA with the Ribo-Zero kit from Epicentre (catalog #RZH1046), followed by use of the TruSeq RNA Sample Prep Kit (catalog #FC-122-1001) following manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RNAseq after non-targeting-RNAi; Replicate 2
|
| Data processing |
RNA-seq analysis was done using TopHat v1.2.0 and Bowtie v0.12.7. Only uniquely mapping reads were used. Fly transcript annotations were from Ensembl 62. Differentially expressed genes after RNAi were called with an adjusted p-value < 0.001 and MA plots were determined by DEseq, v1.4.1. In order to avoid off-target RNAi, independent RNAi experiments, using two different dsRNA regions for each target, were treated as biological replicates for analysis of differential expression.
|
| |
|
| Submission date |
Sep 14, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander (Garrett) Garruss |
| E-mail(s) |
asg@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Shilatifard
|
| Street address |
1000 East 50th Street
|
| City |
Kansas CIty |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE32120 |
The little elongation complex (LEC) regulates small nuclear RNA transcription |
|
| Relations |
| Reanalyzed by |
GSM3274838 |
| SRA |
SRX097627 |
| BioSample |
SAMN00718952 |
