Unknown,Transcriptomics,Genomics,Proteomics

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A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages

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. 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.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Leming Shi

PROVIDER: E-GEOD-53960 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.

Yu Ying Y Fuscoe James C JC Zhao Chen C Guo Chao C Jia Meiwen M Qing Tao T Bannon Desmond I DI Lancashire Lee L Bao Wenjun W Du Tingting T Luo Heng H Su Zhenqiang Z Jones Wendell D WD Moland Carrie L CL Branham William S WS Qian Feng F Ning Baitang B Li Yan Y Hong Huixiao H Guo Lei L Mei Nan N Shi Tieliu T Wang Kevin Y KY Wolfinger Russell D RD Nikolsky Yuri Y Walker Stephen J SJ Duerksen-Hughes Penelope P Mason Christopher E CE Tong Weida W Thierry-Mieg Jean J Thierry-Mieg Danielle D Shi Leming L Wang Charles C

Nature communications 20140101

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 RNA-Seq 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 ge ...[more]

PMID: 24510058

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Project description:Objective: Apolipoprotein E (Apo E) is a multifunctional protein, originally described in the context of lipoprotein metabolism and cardiovascular disease. More recently, anti-inflammatory functions of ApoE have been documented. ApoE was studied in the context of several inflammatory disorders, but its role in the pathogenesis of acute organ rejection is unknown. In this study, we test the hypothesis that ApoE attenuates acute renal allograft rejection. Materials and methods: The Dark Agouti (DA) to Lewis (Lew) and the Brown Norway (BN) to Lew rat strain combinations were used to investigate fatal acute rejection. In addition, Fischer 344 (F344) kidneys were transplanted to Lew rats to study reversible acute rejection. Isograft recipients and untreated Lew rats were used as controls. ApoE mRNA expression was quantified in intravascular leukocytes accumulating in the blood vessels of renal grafts and in graft tissue. Apo E protein levels were assessed in blood plasma. To test the protective potential of ApoE, recipients of BN kidneys were treated with ApoE-mimetic peptide. Results: Intravascular graft leukocytes and renal tissue obtained from animals undergoing reversible acute rejection expressed increased levels of ApoE mRNA, whereas during fatal rejection, ApoE expression remained unchanged in the BN to Lew rat strain combination or was significantly reduced when DA rats were used as donors of the kidney. On the protein level, no changes in ApoE were seen in plasma. However, we do not know if local leukocytic ApoE expression results in increased ApoE concentrations inside graft blood vessels. Peptide treatment of allograft recipients reversed fatal rejection and significantly improved animal survival. Conclusions: ApoE plays a protective role in acute organ rejection. Further studies are needed to understand the exact mechanism how ApoE reverses acute rejection. dual-color balanced dye-swap design with 4 biological replicates, hybridized on 4 arrays

Dataset Information

A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages

Publications

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.

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