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

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

PROVIDER: PRJEB13828 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1395650_1.fastq.gz	Fastqsanger.gz
	ERR1395650_2.fastq.gz	Fastqsanger.gz
	ERR1395641_1.fastq.gz	Fastqsanger.gz
	ERR1395641_2.fastq.gz	Fastqsanger.gz
	ERR1395651_1.fastq.gz	Fastqsanger.gz

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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

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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.

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

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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 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.

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Project description:We performed mRNA sequencing of reciprocal F1 female hybrids from two crosses (362/765 and 517/765) and the parental DGRP lines (362, 517 and 765). Specifically, we aimed to identify whether transcripts predicted to be regulated by cis-eQTLs exhibit a significant allele-specific bias in gene expression. Since both alleles act in the cross in the same trans environment, differential expression in the F1 is a direct measure of cis-regulatory activity.

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