Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats

Abstract

The rat is used extensively by the pharmaceutical, regulatory, and academic communities for safety assessment of drugs and chemicals and for studying human diseases; however, its transcriptome has not been well studied. As part of the SEQC (i.e., MAQC-III) consortium efforts, a comprehensive RNA-Seq data set was constructed using 320 RNA samples isolated from 10 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four ages (2-, 6-, 21-, and 104-week-old) with four biological replicates for each of the 80 sample groups (organ-sex-age). With the Ribo-Zero rRNA removal and Illumina RNA-Seq protocols, 41 million 50 bp single-end reads were generated per sample, yielding a total of 13.4 billion reads. This data set could be used to identify and validate new rat genes and transcripts, develop a more comprehensive rat transcriptome annotation system, identify novel gene regulatory networks related to tissue specific gene expression and development, and discover genes responsible for disease and drug toxicity and efficacy.

Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages

“…Fischer 344 rats across 11 tissues and 4 developmental ages (Yu et al 2014a;Yu et al 2014b). 105 This is an ideal dataset for a systematic comparison of expression values of circRNAs and its 106 cognate mRNAs across tissue types and developmental stages.…”

“…Yu et al (Yu et al 2014a;Yu et al 2014b) constructed and sequenced 320 rRNA-depleted RNA-455 seq libraries containing samples from 11 rat tissue types [adrenal gland, brain, heart, kidney, 456 liver, lung, muscle, spleen, thymus, testes (male only), and uterus (female only)] from both sexes 457…”

“…To overcome above issues, we analyzed the transcriptomes of both mRNAs and 100 circRNAs in a rat BodyMap RNA-seq dataset (Yu et al 2014a;Yu et al 2014b) using Sailfish-cir 101 ), a computational tool that we recently developed, which applies a model-based 102 algorithm to precisely quantify expression level of both linear and circular transcripts from 103 rRNA-depleted RNA-seq data. The rat BodyMap dataset contains 320 samples isolated from 104…”

Effect of ACTH and hCG on the Expression of Gonadotropin-Inducible Ovarian Transcription Factor 1 (Giot1) Gene in the Rat Adrenal Gland

“…These studies were performed on Fischer 344 strain rats aged 2, 6, 21 and 104 weeks [13]. Experimental data were obtained from Gene Expression Omnibus database, accession number: GSE53960 (available at ) (accessed date: 03 August 2018).…”

“…Color of the circle corresponds to the appropriate development stage; ( B ) expression levels of Giot1 gene in entire adrenal glands of Fischer 344 male and female rats in course of ontogenesis. The analysis of data published by Yu [13]. Experimental data was obtained from Gene Expression Omnibus database, accession number: GSE53960 (available at ) (accessed date: 3 August 2018); ( C ) comparison of the level of expression of the Giot1 gene in adrenals and ovaries of adult rats of the Wistar strain.…”