|
| Status |
Public on Dec 12, 2008 |
| Title |
cDNA_(H33_Control_Affymetrix) |
| Sample type |
RNA |
| |
|
| Source name |
H33_Control_Affymetrix
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
S2 cells were harvested and RNA was extracted using the Trizol (Invitrogen) method following the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Drosophila Genome 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Expression in S2 cells
|
| Data processing |
Data processing was performed using Affymetrix GCOS 1.4 software. After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002).
|
| |
|
| Submission date |
Nov 24, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
[email protected]
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE13217 |
Genome-wide profiling of salt fractions maps physical properties of chromatin |
|
| Relations |
| Reanalyzed by |
GSE119084 |
