|
| Status |
Public on Aug 27, 2020 |
| Title |
ctrl_48h_3 |
| Sample type |
SRA |
| |
|
| Source name |
fly heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: day 14
genotype: hs-GAL4
treatment: 48h heat-shock
|
| Treatment protocol |
hs-GAL4, UAS-Fer2::FLAG flies (hs>Fer2::FLAG) were heat-shocked at 37 °C for 3 h, or maintained at 25 °C (untreated), and collected 12 h or 48 h later (N=3 replicates per group). The same procedure was also applied to flies carrying hs-GAL4 but not the UAS-Fer2::FLAG transgene (ctrl), in order to identify and exclude from our analysis the genes that responded to heat irrespective of Fer2 induction.
|
| Growth protocol |
Flies were maintained on standard cornmeal-agar food at 25 °C in a 12 h:12 h light-dark cycle and under controlled humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
50 flies per replicate were frozen in liquid nitrogen and kept at -80 °C until processed. Fly heads were collected using metal sieves. Total RNA was isolated from fly heads using Trizol according to the manufacturer’s instructions and treated with Turbo DNase for 30 min at 37 °C.
Libraries were prepared at the iGE3 Genomics Platform in Geneva. Single reads of 50 bp were generated using an Illumina HiSeq 2500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were mapped to the dm3 genome assembly using TopHat with default settings.
Differentially expressed genes (DEG) analysis was performed using Cufflinks, Cuffmerge and Cuffdiff, to compare flies who received the heat shock treatment with untreated flies. The same analysis was performed on hs-GAL4 flies not carrying the UAS-Fer2::FLAG transgene (ctrl), to identify the genes which responded to heat irrespective of Fer2 induction. These heat-responsive genes were subtracted from DEG identified in the hs>Fer2::FLAG experiment.
Genome_build: dm3
Supplementary_files_format_and_content: table files including relative abundance for each group
|
| |
|
| Submission date |
Aug 26, 2020 |
| Last update date |
Aug 27, 2020 |
| Contact name |
Federico Miozzo |
| Organization name |
University of Geneva
|
| Street address |
30 Quai Ernest-Ansermet, CH-1211
|
| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE156890 |
Identification of genes regulated by Fer2 in the fly brain using an overexpression approach |
| GSE156893 |
Fer2 in the fly brain |
|
| Relations |
| BioSample |
SAMN15912787 |
| SRA |
SRX9008780 |
