|
| Status |
Public on Nov 21, 2012 |
| Title |
AfrFemale-R2 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Sex: female
population: Africa (Zimbabwe)
age: 2-4 days
|
| Treatment protocol |
Adult flies aged 2–4 days were anesthetized on ice and brains were dissected in 1xPBS (phosphate buffered saline) and stored in RNAlater (Qiagen) to prevent RNA degradation
|
| 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. Eight tagged libraries were generated, pooled and run on two lanes of a HiSeq 2000 sequencer (Illumina) to generate single reads of 50 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 5.43) using Stampy (version 1.0.17) and setting --substitutionrate=0.01
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. For calculations of RPKM, the length of the longest transcript of each gene was used
Genome_build: dmel_r5.43
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Sep 14, 2012 |
| 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) |
| GSE40907 |
Population and sex differences in Drosophila melanogaster brain gene expression |
|
| Relations |
| Reanalyzed by |
GSM3281489 |
| SRA |
SRX187182 |
| BioSample |
SAMN01178063 |
