|
| Status |
Public on Dec 01, 2010 |
| Title |
ade2dsRNA-2b |
| Sample type |
RNA |
| |
|
| Source name |
S2 cells+ade2 dsRNA2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells
protocol: RNAi-mediated knockdown of ade2 (ade2 RNAi)
RNAi name: ade2 dsRNA2
|
| Treatment protocol |
dsRNA treatment followed the protocol of Maiato et al (2003) Biol. Proced. Online 5:153-161.
|
| Growth protocol |
S2-6 cells were obtained from the Drosophila Genetics Resources Center and cultured in Schneider cell meda (Invitrogen) supplemented with 10% FBS (Invitrogen)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol (Invitrogen)
|
| Label |
Cy3
|
| Label protocol |
RNA was linearly amplified and labeled with Cy3, and labeled cRNA quantity and specific activity were assessed with the NanoDrop ND-1000 (Thermo Scienctific).
|
| |
|
| Hybridization protocol |
1.65 ug of labeled cRNA was fragmented for 30 min and applied to Agilent microarrays 4x44K format (G2519F) and hybridized for 17 hrs at 65 C in the Agilent hybridization oven, and washed with Agilent wash buffers
|
| Scan protocol |
Agilent DNA Microarray Scanner at 5um resolution
|
| Description |
gene expression after 4 days
ade2dsRNA-2b
|
| Data processing |
Agilent Feature extraction 9.1 software. Intensities per spot had their local background subtracted. A step of spatial detrending was done using negative control spots across the whole array and subtracting a surface fit from the data. Then data were loaded into GeneSpring 7.3 and all raw values below 5 were set to 5. The data were normalized to the median, so that intensities were divided by the median of all intensities.
|
| |
|
| Submission date |
Sep 14, 2010 |
| Last update date |
Sep 14, 2010 |
| Contact name |
Denise Clark |
| E-mail(s) |
[email protected]
|
| Phone |
506-452-6193
|
| Fax |
506-453-3583
|
| Organization name |
University of New Brunswick
|
| Department |
Biology
|
| Street address |
10 Bailey Drive
|
| City |
Fredericton |
| State/province |
NB |
| ZIP/Postal code |
E3B 5A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL7300 |
| Series (1) |
| GSE24123 |
Effects of purine de novo synthesis knockdown on gene expression in Drosophila melanogaster S2 tissue culture cells |
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