|
| Status |
Public on Jul 15, 2011 |
| Title |
Drosophila_aly mutant testis_replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
aly mutant testis, replicate 3
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: aly2/aly5P mutant fly.
time point: 1 day old.
|
| Treatment protocol |
aly mutant testes were dissected in DEPC-treated 1× PBS buffer in 20 min interval, followed by immediate snap freezing in liquid nitrogen.
|
| Growth protocol |
All fly stocks were grown in a 25 °C incubator with standard medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from approximately 200 pairs of fly testes was extracted using TRIzol (Invitrogen, #15596-018, Carlsbad, CA, USA) following the manufacturer's instructions. The genomic DNA was degraded using 2 Units of DNase I (Fermentas, #EN0521, Glen Burnie, MD, USA) at 37°C for 20 minutes. RNA integrity was checked by gel electrophoresis (1% agarose).
|
| Label |
biotin
|
| Label protocol |
Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.
|
| |
|
| Hybridization protocol |
Approximately 4 μg of total RNA from each biological replicate were used to generate labeling probes to hybridize with the Affymetix GeneChip Drosophila Genome 2.0 Array according to the Affymetrix protocol. Three biological replicates were performed for each genotype. Microarray hybridization was processed at the Core Facility at the Stanford University School of Medicine.
|
| Scan protocol |
Scanning was performed with the Affymetrix GeneChip scanner using default settings.
|
| Data processing |
The raw data were exported from the Affymetrix Microarray Suite (MAS). The CEL files were used for signal normalization with RMA as part of the limma package from the Bioconductor R packages (http://www.bioconductor.org).
|
| |
|
| Submission date |
Apr 19, 2011 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Margaret T. Fuller |
| E-mail(s) |
[email protected]
|
| Phone |
(650) 725-7681
|
| Fax |
(650) 725-7739
|
| URL |
http://cmgm.stanford.edu/~fullab/
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Departments of Developmental Biology and Genetics
|
| Lab |
Fuller Lab
|
| Street address |
Beckman Center B300, 279 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5329 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE28728 |
Sequential changes at differentiation gene promoters as they become active in a stem cell lineage |
|
| Relations |
| Reanalyzed by |
GSE68696 |
| Reanalyzed by |
GSM1933156 |
| Reanalyzed by |
GSE119084 |
