|
| Status |
Public on Nov 29, 2010 |
| Title |
dTIP60WT, Biological Rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Drosophila larvae, ubiquitously expressing dTIP60 wild type
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: 35 whole larvae
genotype: GAL4-337 and dTIP60WT parents
|
| Treatment protocol |
Ubiquitous UAS expression with the 337-GAL4 driver.
|
| Growth protocol |
Virgin female w1118, dTIP60E431Q, and dTIP60WT flies were crossed to 337-GAL4 males that express GAL4 ubiquitously at 25°C. Fertilized embryos were collected in 3-hour intervals and incubated at 25°C for three days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from a pool of 35 larvae for each chip using Trizol according to the manufacturer's instructions and was treated twice with Dnase II according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Performed by Seqwright using Affymetrix GeneChip 3' IVT Express Target Amplification, Labeling, and Control kit (Affymetrix Cat. No. 901229): 500 ng of total RNA was used for 1st and 2nd strand cDNA synthesis with oligo-dT containing T7 promoter. This synthesized double-stranded cDNA was used as template to generate Biotin-labeled cRNA, which was fragmented to 35-200 bases in size using fragmentation buffer.
|
| |
|
| Hybridization protocol |
Performed by Seqwright: 10 ug of Biotin-labeled cRNA in 200ul hybridization cocktail was injected onto each array and hybridized at 45°C for 16 hours with rotation of 60 rpm in a GeneChip Hybridization Oven 640 (Affymetrix). Staining and washing of each array was performed on a GeneChip Fluidics Station 450 (Affymetrix) using Streptavidin Phycoerythrin (Invitrogen Cat. No. S866), goat IgG (Sigma Cat. No. I 5256) and Biotinylated anti-streptavidin antibody (Vector Laboratories Cat. No. BA-0500).
|
| Scan protocol |
Performed by Seqwright: Each array was scanned with a GeneChip 7G Plus Scanner (Affymetrix) to acquire the raw image and Affymetrix GCOS software was used to process the data.
|
| Description |
Gene expression data
|
| Data processing |
Expression values were generated in dCHIP using model-based expression algorithms and the perfect match/mismatch model (PM/MM). Array intensities were normalized to the array with median intensity. Probe sets were filtered using a Student's t-test and p<0.05, fold change >2, and a 90% confidence bound. Correlation coefficients showed good agreement between duplicate samples.
|
| |
|
| Submission date |
Nov 28, 2010 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Felice Elefant |
| E-mail(s) |
[email protected]
|
| Phone |
215-895-0220
|
| Organization name |
Drexel University
|
| Department |
Biology
|
| Street address |
3141 Chestnut Street, Stratton Hall 226
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE25635 |
Histone acetylation dependent microarray analysis uncovers a role for Tip60 HAT activity in nervous system function and general metabolism |
|
| Relations |
| Reanalyzed by |
GSE119084 |
