|
| Status |
Public on Aug 31, 2011 |
| Title |
2hr_control_rep3, R/Bioconductor GC-RMA |
| Sample type |
RNA |
| |
|
| Source name |
2hr_male head_control
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: isogenized Canton-S
gender: male
tissue: head
age: 5 days
treatment: exposure to no female fly
treatment time: 2 hours
|
| Treatment protocol |
Virgin males were raised in groups of 20 or fewer flies at 25oC. On day 4, they were transferred to individual vials. On day 5, they were exposed to a virgin female, a cauterized virgin female fly, or no female. 2 hrs after the mated male finished copulating with the female, a male from each group was collected for RNA isolation.
|
| Growth protocol |
Stocks were maintained on cornmeal/sugar media at 25oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol.
|
| Scan protocol |
Standard Affymetrix protocol using an Affymetrix GCS 3000 7G scanner.
|
| Description |
C1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.
|
| Data processing |
All 15 chips were analyzed simultaneously by 4 platforms (5 algorithms): dCHIP, GCOS, Bioconductor, GeneSpring GX 7.3.1. dChip uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-MM and PM procedures under default parameters. Expression values were also computed using the recommended settings in GCOS version 1.2. All probesets were scaled using a TGT value of 500, and no normalization was applied (i.e., the normalization factor was 1.0). We also utilized the GC-RMA model-based algorithm in the R-language platform. Bioconductor provided the open source GCRMA and associated packages. In addition, we used the GCRMA model-based algorithm in GeneSpring GX 7.3.1 (Agilent Technologies). Default normalization was the raw intensity value for each probe set on a chip divided by the overall median intensity value for that chip. This “pre-normalized” value was then divided by the median “pre-normalized” value for that specific probe set across all 15 chips in the experiment.
|
| |
|
| Submission date |
Sep 15, 2010 |
| Last update date |
Aug 31, 2011 |
| Contact name |
Ginger Carney |
| E-mail(s) |
[email protected]
|
| Fax |
979-845-2891
|
| Organization name |
Texas A&M University
|
| Department |
Biology
|
| Street address |
3258 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77845 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
|
