|
| Status |
Public on Dec 10, 2021 |
| Title |
aged_2 |
| Sample type |
RNA |
| |
|
| Source name |
mix of 100 female flies and 100 male flies_aged
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: 45 days-old
Sex: mixed
tissue: Whole organism
|
| Growth protocol |
For each biological replicates 250 virgin females and 250 virgin males were cultured in 10 bottles (50 flies per bottle) containing 10ml of fly food and fresh yeast. The flies were cultured in a 20C degree incubator with standard day/night cycle and 50% humidity. Flies were transfered to fresh bottle every three days. To purify total RNA, 100 males and 100 females were used among 3 days-old flies and then among 45 days-old flies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the RNeasy Mini kit (Qiagen, Valencia, CA) after isolation using TRIzol reagent (Life Technologies, Inc., Grand Island, NY). The purification was performed with whole organism.
|
| Label |
biotin
|
| Label protocol |
All protocols were conducted as described in the NuGEN Ovation User Guide and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 100ng of total RNA were converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region. Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase (Ovation RNA Amplification System V2, NuGEN Inc., San Carlos CA, USA), and the resulting cDNA was assessed by Bioanalyzer, fragmented and biotinylated (Encore Biotin Module, NuGEN Inc., San Carlos CA), followed by the addition of 3.75ug of labeled cDNA to Affymetrix hybridization cocktails.
|
| |
|
| Hybridization protocol |
Target hybridization was performed on GeneChip Drosophila Genome 2.0 arrays (Affymetrix Inc., Santa Clara CA, USA) according to the manufacturer’s procedures in the GeneChip® Hybridization Oven 645, followed by washing and staining in the GeneChip® Fluidics Station 450.
|
| Scan protocol |
Data were acquired with GeneChip® Scanner 3000 7G (Affymetrix, Inc., Santa Clara, CA, USA).
|
| Data processing |
Data analysis was performed using Partek Genomics Suite v6.5 to apply the GCRMA normalization algorithm.
processed_data.txt: Each probe is shown on a separate line. Column A corresponds to the gene symbols associated with the probe. Column B corresponds to Flybase IDs associated with the probe. Column C corresponds to the probe ID. Column D to I corresponds to the log2 scale of the fluorescence intensity recorded for each probe for 3 days-old biological replicates 1-3 and 45 days-old biological replicates 1-3.
|
| |
|
| Submission date |
Nov 03, 2021 |
| Last update date |
Dec 10, 2021 |
| Contact name |
Alexei Tulin |
| E-mail(s) |
alexei.tulin@und.edu
|
| Organization name |
University of North Dakota
|
| Department |
Epigenetics Department
|
| Lab |
Alexei Tulin Lab
|
| Street address |
501 N Columbia Rd Stop 9061
|
| City |
Grand Forks |
| State/province |
North Dakota |
| ZIP/Postal code |
58203-2898 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE187896 |
Age-related changes of gene expression profiles in Drosophila |
|
