|
| Status |
Public on Dec 31, 2013 |
| Title |
Canton S, wildtype, whole brain, new, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Drosophila adult_Canton S, wildtype, whole brain, new
|
| Organism |
Drosophila melanogaster |
| Characteristics |
gender: female and male
developmental stage: adult
genetic background: Canton S
genotype/variation: WT_new
tissue: brain
|
| Treatment protocol |
Brains were dissected under PBS and transferred directly to a chilled tube containing RNA lysis buffer.
|
| Growth protocol |
All flies were raised and maintained on standard cornmeal molasses agar at 16˚C or room temperature.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Ambion RNAqueous Micro columns and amplified using the NuGEN Ovation FFPE WTA System V3.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared using the NuGEN Encore Biotin Module kit from 3.5ug amplified RNA.
|
| |
|
| Hybridization protocol |
The entire fragmented, labeled cDNA fraction was placed into a hyb cocktail volume of 150uL; 130uL were hybridized for 18-20 hr at 45C on GeneChip Drosophila Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS3000 scanner.
|
| Description |
WT_new_2
4 brains total containing both male and female flies
amplified total RNA
|
| Data processing |
Using the R package affy, raw data was processed using RMA. P/M/A calls were extracted using affy, and probes were kept for statistical analyses if greater than 50% of replicates in at least one sample were called present. Of the 18,952 total probes, 13,290 were used for statistical analyses. Differentially expressed genes were determined using the R package limma with an FDR-adjusted p-value of 0.05 as the cutoff for determining statistical significance. Given the presence of batch effects and genetic background effects, we took the lists of differentially expressed genes for WT_new/C17 and WT_new/PMdr65 and subtracted genes that also showed up in the lists of differentially expressed genes between WT_new/WT_old and WT_new/UAS_control.
|
| |
|
| Submission date |
May 01, 2013 |
| Last update date |
Dec 31, 2013 |
| Contact name |
Michael DeSalvo |
| E-mail(s) |
[email protected]
|
| Organization name |
UC San Francisco
|
| Department |
Department of Anesthesia
|
| Lab |
Roland Bainton
|
| Street address |
600 16 St Box 2200
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158-2200 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE46550 |
Homeostatic interactions between chemoprotective functions at the blood-brain barrier |
|
