|
| Status |
Public on Apr 25, 2017 |
| Title |
50EH2 |
| Sample type |
SRA |
| |
|
| Source name |
50h_without rivals_head+thorax
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Dahomey
genotype/variation: wild type
Sex: male
sample group: without rivals
time point: 50h
tissue: head+thorax tissue
|
| Treatment protocol |
Rival wild type males were then introduced to the focal males for 2, 26 or 50h.
|
| Growth protocol |
Dahomey wild type males were raised at a density of 100 larvae per vial on SY medium (100g brewer’s yeast powder, 100g sugar, 20g agar, 30ml Nipagin (10% solution) and 3ml propionic acid per litre of medium). Upon eclosion, males were stored 10 per vial and then at 1d old placed in individual vials for 5days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Focal males were then snap frozen in liquid nitrogen. Prior to RNA extraction, males were separated into abdomen and Head+Thorax body parts. RNA was extracted (MiRVana kit) from pools of n = 40 male body parts and sent for RNA sequencing (Illumina HiSeq, 50 cycles, non directional, 4 samples per lane). Differential expression of transcripts was validated by using qRT-PCR onall three replicates of the same biological samples.
Baseclear provider, mRNA-Seq Library preparation using standard TruSeq library protocol. RNA sequencing = 50 cycles, single-read 4 samples per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 22
|
| Data processing |
we kept for further analysis, only the reads which did not contain Ns (99% of the reads)
the reads were mapped to the D. melanogaster genome (v5.46), using PatMaN (Prueffer et al 2008), full length, no mis-matches allowed.
for comparison purposes, the reads in every sample were resampled to a fixed total (the method is called bootstrapping normalization and is presented in the accompanying manuscript)
the expression levels were obtained as indicated in Mortazavi et al 2008
the differential expression was first determined between tissues (HT vs A) and next between the treatments (with vs without rivals)
Genome_build: D. melanogaster v 5.46, www.flybase.org
Supplementary_files_format_and_content: csv files which contain the gene expression levels.
|
| |
|
| Submission date |
Mar 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
irina.mohorianu@paediatrics.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Medical Sciences Division
|
| Lab |
Oxford Vaccine Group
|
| Street address |
Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7LE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE55839 |
Differential gene expression following exposure to rivals in male Drosophila melanogaster. |
|
| Relations |
| Reanalyzed by |
GSM3285279 |
| BioSample |
SAMN02688169 |
| SRA |
SRX485423 |
