Landscape of rat microRNA BodyMap across 11 organs, four ages, and two sexes
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ABSTRACT:
PROVIDER: PRJNA722666 | ENA |
REPOSITORIES: ENA
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Project description:The rat has been used extensively as a model system for biological studies. However, its microRNA (miRNA) transcriptome has not been well established. Here, we constructed a comprehensive rat miRNA BodyMap based on miRNA-seq of 320 samples from 11 organs of both sexes of juvenile, adolescent, adult, and aged Fischer 344 rats. We quantified the expression profiles of 993 rat miRNAs, including 268 novel miRNA candidates. A large number of miRNAs showed organ-specific, age-dependent, or sex-specific expression patterns. Particularly, brain exhibited the strongest organ-enriched expression patterns, and testis showed the most strikingly age-dependent expression patterns. Interestingly, the expression levels of two clusters of miRNAs were highly correlated with those of mRNAs and were highly age dependent. The miRNA dataset along with previously reported mRNA data from the same set of samples represents a unique resource to improve understanding of rat transcriptome and subsequently better utilize rats for biomarker discovery.
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Project description: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.
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Project description:Aging progress is distinctly characterized by systematic and progressive decline of physiological functions with increasing age in virtually all tissues or organs. Addressing the patterns of molecular changes in different tissues and how different tissues interact with each other during aging are an important question in aging. This study sampled seven tissues at four ages in rats to measure genome-scale gene expression, which allows global insight into coordination, specificity and/or commonness among different tissues with aging progress.
2011-09-01 | GSE23328 | GEO
Project description: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.
2014-02-14 | GSE53960 | GEO
Project description:Aging progress is distinctly characterized by systematic and progressive decline of physiological functions with increasing age in virtually all tissues or organs. Addressing the patterns of molecular changes in different tissues and how different tissues interact with each other during aging are an important question in aging. This study sampled seven tissues at four ages in rats to measure genome-scale gene expression, which allows global insight into coordination, specificity and/or commonness among different tissues with aging progress. We sampled seven different tissues or organs of male Sprague Dawley rats including hypothalamus, pituitary, adrenal gland, spleen lymphocytes, liver, kidney, and bone at successive ages of 4, 10, 18, and 24 months. For each age, ten individual rats were obtained and seven tissues from the same individual rat were derived every time, and the 5µg of each extracted RNA sample of the same tissue from ten individual rats was equally mixed, then the total amount of 15 µg RNA from this mixture was hybridized to Affymetrix RAE230A GeneChip.
2011-08-31 | E-GEOD-23328 | biostudies-arrayexpress