NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE60314 Query DataSets for GSE60314
Status Public on Dec 21, 2015
Title mRNA sequence data of individual Drosophila melanogaster male and female flies from 16 Drosophila Genetic Reference Panel lines reared in replicated environments
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Summary Our primary objective was to characterize the amount of variation in transcript abundance among individual flies with identical genotypes. We also wanted to determine which analysis methods would be optimal for RNA-Seq data. To meet these objectives, we performed transcriptional profiling of whole adult individuals from 16 Drosophila Genetic Reference Panel (DGRP) lines. We quantified differential expression among genotypes, environments, and sexes.
 
Overall design We randomly chose 16 DGRP lines for this experiment: DGRP-93, DGRP-229, DGRP-320, DGRP-352, DGRP-370, DGRP-563, DGRP-630, DGRP-703, DGRP-761, DGRP-787, DGRP-790, DGRP-804, DGRP-812, DGRP-822, DGRP-850, and DGRP-900. We collected 8 virgin male and 8 virgin female flies from the 16 DGRP genotypes in three replicated environments to produce RNA sequence profiles. We controlled the environmental conditions in the following ways. We seeded the fly cultures with 5 male and 5 female parents. We reared the progeny in a single incubator on standard Drosophila food (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/bloomfood.htm) at 25°C, 60% humidity, and a 12:12-hour light:dark cycle. We collected and maintained male and female virgins at 20 flies to a same-sex vial for four days prior to RNA extraction to control for social exposure. Flies were frozen for RNA extraction at the same circadian time (1:00 pm) in 96-well plates. PolyA RNA stranded libraries were prepared by modifying an existing protocol. ERCC (External RNA Controls Consortium, SRM2374, beta version, pools 78A/78B) sequences were added during the library preparation as a control. For some samples >1 library was generated to check technical variation. We performed multiplexed single-end 76 bp sequencing on an Illumina HiSeq2000. Reads were mapped to FlyBase release 5 version 57 and release 6 version 01 of the Drosophila melanogaster genome and the ERCC sequences. Mapped reads were counted at the gene level.
 
Contributor(s) Golovnina K, Chen Z, Lin Y, Sultana H, Oliver B, Harbison S
Citation(s) 26732976, 27770026
Submission date Aug 11, 2014
Last update date Mar 26, 2020
Contact name Brian Oliver
E-mail(s) briano@nih.gov
Phone 301-204-9463
Organization name NIDDK, NIH
Department LBG
Lab Developmental Genomics
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (851)
GSM1470889 DGRP804 F_E1_8_L1
GSM1470890 DGRP804 F_E1_5_L1
GSM1470891 DGRP804 F_E1_2_L1
Relations
BioProject PRJNA258012
SRA SRP045429

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60314_5_57_HTSeq_raw_read_counts.txt.gz 14.3 Mb (ftp)(http) TXT
GSE60314_6_01_HTSeq_raw_read_counts.txt.gz 14.4 Mb (ftp)(http) TXT
GSE60314_ERCC_reference.fa.gz 27.1 Kb (ftp)(http) FA
GSE60314_GEO_run_summary.xlsx 150.9 Kb (ftp)(http) XLSX
GSE60314_dme5_57_ERCC.gtf.gz 2.2 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap