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Sample GSM1004618 Query DataSets for GSM1004618
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

Supplementary file Size Download File type/resource
GSM1004618_AfrFemale-R2.txt.gz 213.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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