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MRNA sequence data of individual Drosophila melanogaster male and female flies from 16 Drosophila Genetic Reference Panel lines reared in replicated environments

ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE60314 | GEO | 2015/12/21

SECONDARY ACCESSION(S): PRJNA258012

REPOSITORIES: GEO

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mRNA sequence data of individual Drosophila melanogaster male and female flies from 16 Drosophila Genetic Reference Panel lines reared in replicated environments

Project description: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. 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 25Â°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.

2015-12-21 | E-GEOD-60314 | biostudies-arrayexpress

Quantification of RNA editing in the Drosophila Genetic Reference Panel

Project description:We report the application of mmPCR-seq to male whole body samples from 131 strains of the DGRP. We quantified RNA editing at 605 different loci using a microfluidic multiplex PCR method coupled with deep sequencing.

2015-08-06 | GSE67082 | GEO

Extensive tissue-specific, circadian molecular variation in a Drosophila Genetic Reference Panel

Project description:We report a large-scale transcriptomic analysis of several tissues of a reference Drosophila melanogaster strain as well as 141 Drosophila Genetic Reference Panel (DGRP) lines at high temporal resolution. Comprehensive data analysis has identified thousands of genes under clock- and tissue-specific control. By using a molecular time table approach, we uncovered that >20% of probed DGRP lines exhibit aberrant circadian expression, and the genetic dissection of one line (DGRP-796) revelled disrupted circadian gene expression in all analysed tissues, revealing a novel deletion in the cry gene. Together, this study revealed extensive variation in tissue-specific circadian expression, which acts upon tissue-specific regulatory networks to generate local oscillations in gene expression. Moreover, the many other lines identified here can be now used to better understand the mechanisms underlying the molecular clock, from tissue-specific to more central mechanisms.

2020-12-10 | GSE126018 | GEO

Quantification of RNA editing in the Drosophila Genetic Reference Panel

2015-08-06 | E-GEOD-67082 | biostudies-arrayexpress

Whole genome sequencing of a panel of genetically diverse crosses of Drosophila melanogaster

Project description:Whole genome sequencing of 8 F1 Drosophila lines along with the two parental lines for one of the F1 genotypes. Data were sequenced to verify previously published genome sequences (parental lines: DGRP, maternal line: PMID31308546) and to identify potentially unbalanced SNPs within the data that might confound allele-specific measurements in the F1 lines.

2020-12-04 | E-MTAB-8877 | biostudies-arrayexpress

Wing disc transcriptomic variation from 32 Drosophila genetic reference panel (DGRP) lines selected for a broad range of wing sizes

Project description:We performed RNA sequencing of wing discs at the wandering L3 larval stage from 32 inbred lines of Drosophila genetic reference panel (DGRP) that consists of 16 big and 16 small wing lines. We aimed to understand system-wide gene regulatory mechanisms that attain the observed natural variation in wing size including the sexual size dimorphism.

2019-02-18 | E-MTAB-7662 | biostudies-arrayexpress

The Drosophila melanogaster Genetic Reference Panel.

Project description: Not available

| S-EPMC3683990 | biostudies-literature

Drosophila Genetic Reference Panel (DGRP) F1 RNA-seq - a comparison to 3prime-tag-seq variance decomposition analysis

Project description:Crosses were carried out between two pairs of lines from the Drosophila Genetic Reference Panel (DGRP): Line 765 (mother) x Line 517 (father) and Line 517 (mother) x Line 362 (father). Embryos resulting from these crosses (as well as from each of the parental lines) was collected at three stages of development: 2-4h, 6-8h, and 10-12h after egg laying. Following standard procedure, three, one-hour pre-lays were collected prior to the experiment (to synchronise embryo age) and all collections were done at 25C. Collections were also made of the reciprocal crosses at 2-4h after egg laying. To validate the variance decomposiiton analysis, we focused our attention on the primary F1 crosses 765 x 517 and 517 x 362. Estimates of line-specific expression, and associated methods, can be found as supplements to Cannavo et al.

2017-01-10 | E-MTAB-4694 | biostudies-arrayexpress

A Genomic Reference Panel for Drosophila serrata.

Project description: Not available

| S-EPMC5873922 | biostudies-literature

Genetic basis of transcriptome diversity in Drosophila melanogaster

Project description:This project uses pooled poly A (+) RNA from the DGRP to derive transcript models specific to DGRP. The derived transcript models provide the basis for quantifying gene expression in the DGRP lines using genome tiling arrays.

2015-10-01 | GSE67505 | GEO

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