Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA574592 | ENA |
REPOSITORIES: ENA
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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 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.
2015-12-21 | E-GEOD-60314 | biostudies-arrayexpress
Project description:Drosophila melanogaster mutation accumulation lines
| PRJNA91737 | ENA
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
Project description:Genome sequencing of six Drosophila melanogaster lines for the study of copy number variations
| PRJNA282433 | ENA
Project description:Drosophila melanogaster 2nd chromosome substitution lines
| PRJNA113409 | ENA
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
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
Project description:Study of context-specific regulation during different developmental time windows of Drosophila melanogaster embryogenesis. Single cell chromatin accessibility was profiled by sciATAC-seq in F1 hybrid embryos obtained by crossing males from four genetically distinct inbred lines from the DGRP collection (Mackay et al. 2012) to females from a common maternal “virginizer” line. F1 embryos were profiled at three key stages of embryonic development: 2-4 hours, 6-8 hours and 10-12 hours after egg laying.
2021-12-21 | E-MTAB-10240 | biostudies-arrayexpress
Project description:Experiment to estimate mutatational variance of gene expression in Drosophila melanogaster at two times in development using 12 mutation accumulation lines. Keywords = evolution Keywords = quantitative genetics Keywords = Drosophila Keywords = mutation Keywords: other
2005-09-04 | GSE2126 | GEO
Project description:Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive, but is essential for predicting adaptive evolution, selecting agriculturally important animals and crops, and personalized medicine. Here, we quantified genome-wide genetic variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel. We found that a substantial fraction of the Drosophila transcriptome is genetically variable and organized into modules of genetically correlated transcripts, which provide functional context for newly identified novel transcribed regions. We identified regulatory variants for the mean and variance of gene expression, both of which showed oligogenic genetic architecture. Expression quantitative trait loci the mean, but not the variance, of gene expression were concentrated near genes. This comprehensive characterization of transcriptomic diversity and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.
2015-10-05 | E-MTAB-3216 | biostudies-arrayexpress