GSM2113223: dgriZA27Z3_f_wb_R4; Drosophila grimshawi; RNA-Seq - SRA

SRX1689258: GSM2113223: dgriZA27Z3_f_wb_R4; Drosophila grimshawi; RNA-Seq
2 ILLUMINA (Illumina HiSeq 2000) runs: 29.9M spots, 2.3G bases, 1.4Gb downloads

Submitted by: NCBI (GEO)

Study: Expression profiling Hawaiian Drosophila species, tissues, and sexes

PRJNA317989 • SRP073087 • All experiments • All runs

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This is a prepublication dataset that should change as updates are made to the underling genomes and annotations. Additional samples may be deposited and some samples may fail quality control. Please contact Haiwang Yang <haiwang.yang@nih.gov> for details. The RNA-seq data set contains the transcriptional profiling of eight sexed tissue types (head, thorax, carcass, abdomen w/o gonad, gonad, other reproductive tract, genitalia, and digestive system) and/or whole adult flies from five strains of Drosophila grimshawi, two strains of D. silvestris, and one strain each of D. hemipeza, D. heteroneura, and D. hawaiiensis. Overall design: Samples were collected in duplicate to quadruplicate from sexually mature sexed adults (4-5 weeks post eclosion), which had been allowed to freely mate. Single-end stranded 76bp PolyA+ RNA-seq was performed on all samples. Libraries were multiplexed with indexed adaptors, and some were also prepared as mixed libraries with RNA from genetically distant species: Drosophila melanogaster (GSE81142) and Anopheles stephensi (GEO entry in preparation). All whole adult samples were prepared from single flies. Tissues were pooled from 3-5 individuals depending on the size of both the tissue and the species. For the G1 strain (reference assembly strain) of D. grimshawi, we profiled seven adult tissues for each sex in addition to whole flies. Samples were whole fly (one fly per sample), head (5 flies), thorax (5 flies), abdomen w/o gonad (5 flies), gonad (testes or ovaries) (5 flies), other reproductive tract (accessory gland and male reproductive duct or female spermatheca and oviduct; 10 flies per sample), genitalia (10 flies), and digestive system (proventriculus, crop, salivary gland, gut, and renal tubule; 5 flies). We prepared sexed single fly whole body samples in quadruplicate for ZA27Z2, ZA27Z3, and Mo010 strains of D. grimshawi. We also prepared sex-specific head, carcass, gonad, other reproductive tract with genitalia with duplicate for Wm1041 strain of D. grimshawi and other species - D. silvestris (Y11R6 and U26B9 strains), D. hemipeza (W40B14 strain), D. heteroneura (W48B6 strain), and D. hawaiiensis (Y17P5 strain). We used reduced number of flies for the non-grimshawi species (i.e., 3 heads, gonads or carcasses per sample, and 6 reproductive tracts plus genitalia per sample).

Sample: dgriZA27Z3_f_wb_R4

SAMN04632178 • SRS1383804 • All experiments • All runs

Organism: Drosophila grimshawi

Library:

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Construction protocol: Flies were anesthetized by briefly chilling on a 0oC glass plate. All samples were dissected in Phosphate Buffered Saline solution pH7.4 and transferred to 112ul of RNA later (Life Technologies, Carlsbad, CA) in 96-well plates at room temperature after being macerated with forceps. After transport, plates were stored at -80oC. For D. grimshawi samples, we added 20-30 1.0mm glass beads (BioSpec Products, Bartlesville, OK) to each sample and added 600ul RLT buffer from the RNeasy 96 kit (Qiagen, Valencia, CA) to each well. We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville, OK). Extraction of total RNA was performed using the RNeasy 96 kit according to manufacturer's guide (spin version), except that we used 712μl of 70% ethanol in each well to dilute the RNAlater and RLT buffer. D. grimshawi RNA was added to D. melanogaster RNA and A. stephensi embryos for homogenization and a second round of RNA extraction using the RNeasy kit. D. melanogaster and A. stephensi RNAseq will be reported elsewhere. Four head and gonad samples of Wm1041 were split into mixed-species and single-species RNA preparations. All other samples were prepared without mixing with other species using the same RNeasy protocol. RNA was quantified using the Quant-iT RiboGreen quantification kit Life Technologies, Carlsbad, CA). We used the Truseq PolyA+ and stranded mRNA kit with half volumes (Illumina, San Diego, CA). 100ng total RNA was input for all samples. We also added 20pg Pool 78A or 78B ERCC spike-ins (Jiang et al., Genome Research, 2011, PMID 21816910) added to the Fragment-Prime-Finish Mix during mRNA fragmentation step. Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA), and pooled for multiplexed sequencing.

Experiment attributes:

GEO Accession: GSM2113223

Links:

NCBI link: NCBI Entrez (gds)

Runs: 2 runs, 29.9M spots, 2.3G bases, 1.4Gb

Run	# of Spots	# of Bases	Size	Published
SRR3355287	15,260,958	1.2G	741.3Mb	2016-06-01
SRR7253580	14,651,928	1.1G	710.1Mb	2018-06-04

ID:: 2424034

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