|
| Status |
Public on Jun 18, 2012 |
| Title |
OPNM_0407_26-Organpipe-Rep2 |
| Sample type |
RNA |
| |
|
| Source name |
OPNM_0407_26, organpipe
|
| Organism |
Drosophila mojavensis |
| Characteristics |
host race: mainland Sonoran
line: OPNM_0407_26
tissue: larvae
developmental stage: third instar
cactus host treatment: organpipe
|
| Treatment protocol |
The nine D. mojavensis lines were reared in either necrotic organpipe or agria cactus. The cactus necroses were created using natural microflora. The procedure for creating the lab necroses followed that of Matzkin et al. 2006 (PMID 17107489).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using Invitrogen’s PureLink Micro-to-Midi Total Purification System. The suggested manufacturer’s instructions were followed, which included a DNase I digestion to remove any possible genomic DNA contamination. The quality and concentration of the RNA was determined using a NanoDrop spectrophotometer (NanoDrop Technologies).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_26, replicate 2.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Feb 20, 2012 |
| Last update date |
Jun 18, 2012 |
| Contact name |
Luciano Matias Matzkin |
| E-mail(s) |
lmm0015@uah.edu
|
| Phone |
256-824-4326
|
| Organization name |
University of Alabama in Huntsville
|
| Department |
Biological Sciences
|
| Street address |
301 Sparkman Drive
|
| City |
Huntsville |
| State/province |
Alabama |
| ZIP/Postal code |
35899 |
| Country |
USA |
| |
|
| Platform ID |
GPL8596 |
| Series (1) |
| GSE35937 |
Population transcriptomics of cactus host shifts in Drosophila mojavensis |
|
