|
| Status |
Public on Oct 18, 2010 |
| Title |
NELF-depleted DGRC S2 Cells, Replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
DGRC S2 Cells, NELF-depleted
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells (DGRC)
|
| Treatment protocol |
For RNAi experiments, S2 cells (DGRC) were harvested 96 hours after addition of dsRNA targeting NELF (NELF-B and NELF-E subunits; NELF-depleted), β-galactosidase (Mock-treated), or no addition (Untreated), as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-73.
|
| Growth protocol |
S2(DGRC) cells were grown in M3 media (Sigma) supplemented with bacto-peptone and yeast extract + 10% FBS (GIBCO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNeasy RNA extraction kit (QIAGEN), with on-column DNAse digestion, 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 |
15ug 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.
|
| Data processing |
Affymetrix GeneChip Command Console (V. 1.1), Algorithm: ExpressionStat 5.0
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 (2006). Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.
|
| |
|
| Submission date |
Sep 15, 2010 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Karen Adelman |
| E-mail(s) |
karen_adelman@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry and Molecular Pharmacology
|
| Street address |
45 Shattuck St. LHRRB-201a
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (2) |
| GSE20472 |
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation |
| GSE24133 |
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation: Expression data |
|
| Relations |
| Reanalyzed by |
GSE119084 |
