U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX471466: GSM1328567: SEQC_Kdn_F_002_3; Rattus norvegicus; RNA-Seq
2 ILLUMINA (Illumina HiSeq 2000) runs: 41.5M spots, 2.1G bases, 1.4Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages
show Abstracthide Abstract
The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNASeq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model. Overall design: We constructed a comprehensive RNA-Seq data set for studying the dynamics of the rat transcriptome using 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old). Four biological replicates were used for each of the 80 sample groups.
Sample: SEQC_Kdn_F_002_3
SAMN02642759 • SRS558212 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Each whole organ was individually ground (mortar and pestle, under continuous liquid N2 chilling) into a fine powder prior to RNA extraction, with the exception of liver, spleen, and gastrocnemius muscle for which approximately 100 mg was ground. Ground organ tissue was stored at -80ºC. Total RNA was extracted from approximately 30 mg of ground tissue by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including treatment with DNase. RNA libraries were prepared for sequencing using an rRNA depletion protocol using the Ribo-Zero Nonmagnetic Kit (Epicentre) coupled with the Illumina TruSeq RNA-Seq library protocol using TruSeq RNA Sample Preparation Kit (Illumina).
Experiment attributes:
GEO Accession: GSM1328567
Links:
External link:
Runs: 2 runs, 41.5M spots, 2.1G bases, 1.4Gb
Run# of Spots# of BasesSizePublished
SRR117009519,058,501952.9M685.8Mb2014-06-20
SRR117009622,426,1411.1G795Mb2014-06-20

ID:
651715

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...