Salaria pavo transcriptome assembly and gene expression - SRA

SRX1948765: Salaria pavo transcriptome assembly and gene expression
1 ILLUMINA (Illumina HiSeq 2000) run: 23.7M spots, 4.7G bases, 3Gb downloads

Design: Total RNA was extracted from whole brain tissue for each individual of the four phenotypes. Samples were transferred to 1 ml of QIAzol lysis reagent (Qiagen) and the tissue homogenized (on ice) with a sonicator (Sonopuls HD 2070; Bandelin, Berlin, Germany) during 30 s at 20-30% power. RNA was then extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) following manufacturer’s protocol. RNA quality and concentration for each sample were determined using a NanoDrop 1000 spectrophotometer (Thermo Scientific). Equal amounts of RNA from each individual were used to prepare the RNA pools corresponding to the high and low GSI libraries for each phenotype. For expression analysis, preparation and sequencing of the eight pooled RNA libraries was performed by The Genome Analysis Centre (Norwich, United Kingdom). Upon arrival, samples’ RNA integrity was first verified on Agilent 2100 Bioanalyzer. Libraries were prepared from polyA+ RNA and sequenced in two lanes on the Illumina HiSeq 2000 as paired-end 100 bp reads with an approximate insert size of 341 bp. Each library was sequenced at a high depth in order to detect transcripts that can become under-represented when analysing whole brain tissue expression. To improve the de novo assembly, four additional pooled libraries, one for each phenotype, were also prepared using RNA from the previous collection, and sequenced using Roche’s 454 technology. Library preparation and single-end sequencing on a GS-FLX System were performed at Max Planck Institute (Berlin, Germany) using the manufacturer's protocol.

Submitted by: Instituto Gulbenkian de Ciencia

Study: Salaria pavo brain transcriptome assembly and gene expression

PRJNA329073 • SRP078494 • All experiments • All runs

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De novo transcriptome assembly and gene expression analysis for whole brain tissue of females and male morphotypes (nest-holder, transitional and sneaker) of the peacock blenny Salaria pavo. Samples were collected during reproductive season.

Sample: Generic sample from Salaria pavo

SAMN05390600 • SRS1563932 • All experiments • All runs

Organism: Salaria pavo

Library:

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: PAIRED

Spot descriptor:

1 forward101 reverse

Runs: 1 run, 23.7M spots, 4.7G bases, 3Gb

Run	# of Spots	# of Bases	Size	Published
SRR3922160	23,652,592	4.7G	3Gb	2017-09-16

ID:: 2805823

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