|
| Status |
Public on Nov 11, 2007 |
| Title |
NELF-depleted 0612_Dm_S2_NELF-depleted_1 |
| Sample type |
RNA |
| |
|
| Source name |
Drosophila melanogaster S2 cells that have been depleted of the NELF complex using dsRNA targeting NELF-B and NELF-E, 96 hour treatment
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Drosophila melanogaster S2 cells, male, largely tetraploid
|
| Biomaterial provider |
Drosophila melanogaster S2 cells were obtained from the Drosophila Genomics Resource Center
|
| Treatment protocol |
Cells were untreated, or treated with dsRNA for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-79
|
| Growth protocol |
Cells were grown in Shields and Sang medium, supplemented with bactopeptone and yeast extract, plus 10% Fetal Bovine Serum, as recommended by the Drosophila Genomics Resource Center
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen) was used, according to manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.
|
| Scan protocol |
Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
|
| Description |
Gene expression analysis was conducted using Drosophila Genome 2.0 Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
|
| Data processing |
The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 6.0). This system performs data pre-processing and error modeling as described in Weng (2004). Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.
|
| |
|
| Submission date |
Dec 26, 2006 |
| Last update date |
Aug 28, 2018 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
microarray@niehs.nih.gov, liuliw@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE6714 |
RNA polymerase is poised for activation across the genome |
|
| Relations |
| Reanalyzed by |
GSE119084 |
