Mesocricetus auratus organs mixture EST library - SRA

SRX373031: Mesocricetus auratus organs mixture EST library
1 LS454 (454 GS FLX Titanium) run: 1.2M spots, 426.7M bases, 269.5Mb downloads

Design: The eighteen total RNA samples were pooled equally into one pool. The total RNA pool underwent additional cleaning using the mirVana isoltation kit following manufacturer’s recommendations (Ambion). Poly A RNA cDNA was synthesized according to a standard protocol using an oligo(dT)-linker primer for first strand synthesis. The N0 cDNA was PCR amplified during 18 cycles using a high fidelity DNA polymerase. Normalization was carried out by one cycle of denaturation and reassociation of the cDNA, resulting in N1-cDNA. Reassociated ds-cDNA was separated from the remaining ss-can (normalized cDNA) by passing the mixture over a hydroxylapatite column. After hydroxylapatite chromatography, the ss-cDNA was amplified with 15 PCR cycles. For 454 sequencing, cDNA in the size range of 500-700 bps was eluted from a preparative agarose gel. An aliquot of the size fractionated cDNA was analyzed on a 1.5% agarose gel. 454 adaptors were ligated to the size fractionated N1 cDNA and 3' fragment sequenced on a Roche 454 using GS FLX technology with Titanium series chemistry following manufacturer’s recommendations.

Submitted by: UNIVERSITY OF WASHINGTON (NREMC)

Study: Mesocricetus auratus organs mixture EST library

PRJNA226253 • SRP032520 • All experiments • All runs

show Abstracthide Abstract

An expressed sequence tag (EST) library derived from mRNA and snRNA isolated from the brains, lungs, spleens, kidneys, livers, and hearts of adult female Syrian hamsters was sequenced. The assembled library represents a total of 60,117,204 nucleotides, which is expected to be approximately a third of the Syrian hamster transcriptome. Our Mesocricetus auratus library mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. Finally, ESTs of the library have been aligned over a compendium of 17 rodents, primate and laurasiatheria species to gain insights about the genomic evolution of this species.

Sample: Mesocricetus auratus Organ Mixture

SAMN02390920 • SRS498473 • All experiments • All runs

Organism: Mesocricetus auratus

Library:

Instrument: 454 GS FLX Titanium

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: unspecified

Layout: SINGLE

Spot descriptor:

5 forward

Links:

NCBI link: NCBI Entrez (pubmed)

Runs: 1 run, 1.2M spots, 426.7M bases, 269.5Mb

Run	# of Spots	# of Bases	Size	Published
SRR1024010	1,212,395	426.7M	269.5Mb	2014-11-03

ID:: 533244

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