|
| Status |
Public on Dec 22, 2011 |
| Title |
ELL-rnai affy rep2 |
| Sample type |
RNA |
| |
|
| Source name |
S2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
knockdown: ELL
cell line: S2
|
| 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. RNAi was performed with the ELL-A dsRNA. A region of the B-lactamase gene was used as a nontargeting control.
|
| 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.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was done starting with 1 ug of total RNA using Ambion's MessageAmp II-Biotin Enhanced Kit (cat#1791).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Drosophila Genome 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned with GeneChip 3000.
|
| Data processing |
Affymetrix Drosophila Genome 2 arrays were analyzed in R, version 2.11.1, using the packages affy (Gautier et al., 2004), version 1.26.1, and limma (Smyth et al., 2005), version 3.4.3. Normalization was done using rma. Annotation information for the probes was taken from Ensembl 62.
|
| |
|
| Submission date |
Dec 20, 2011 |
| Last update date |
Aug 28, 2018 |
| 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 |
GPL1322 |
| Series (1) |
| GSE32120 |
The little elongation complex (LEC) regulates small nuclear RNA transcription |
|
| Relations |
| Reanalyzed by |
GSE119084 |
