|
| Status |
Public on Nov 28, 2016 |
| Title |
E14CS3 |
| Sample type |
SRA |
| |
|
| Source name |
whole flies
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Sex: male
population: Europe
line: E14
condition: cold shock (3.5h)
|
| Treatment protocol |
Flies were exposed to a 0°C cold shock for 7h and then brought back to room temperature for recovery
|
| Growth protocol |
All flies were maintained on standard cornmeal-molasses medium at 22° with a 14 h light:10 h dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction and DNase I digestion were performed using the MasterPure RNA Purification Kit (Epicentre)
Poly-A mRNA was purified and fragmented by sonication. First strand single end cDNA was synthesized using random primers. Tagged libraries were generated, pooled and run on a HiSeq 2000 sequencer (Illumina) to generate single reads of 51 bases
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Standard Illumina pipeline using Bustard for basecalling
Illumina sequence reads were mapped to the reference D. melanogaster transcriptome (FlyBase release 5.57) using NextGenMap (version 0.4.12) and requiring a minimum of 40 mapped residues (option –R 40)
Expression was quantified on a “per gene” basis. For this, if a sequence read mapped to one or more transcripts of the same gene, it was counted as one “hit” for that gene and all subsequent analyses were performed at the gene level
Genome_build: dmel_r5.57
Supplementary_files_format_and_content: tab-delimited text files include gene specific read counts for each sample
|
| |
|
| Submission date |
Jan 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephan Hutter |
| Organization name |
University of Munich
|
| Department |
Department of Biology II
|
| Lab |
Section of Evolutionary Biology
|
| Street address |
Grosshaderner Strasse 2
|
| City |
Planegg-Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE77404 |
Canalization of gene expression is a major signature of regulatory cold adaptation in temperate "Drosophila melanogaster" |
|
| Relations |
| Reanalyzed by |
GSM3278361 |
| BioSample |
SAMN04448547 |
| SRA |
SRX1553901 |
