Landscape of rat microRNA BodyMap across 11 organs, four ages, and two sexes
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE172269 | GEO | 2021/11/01
REPOSITORIES: GEO
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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.
2014-02-14 | GSE53960 | 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. 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.
2014-02-14 | E-GEOD-53960 | biostudies-arrayexpress
Project description:Global miRNA expression was examined in liver tissues from male and female F344 rats over the life span for the purpose of evaluating their possible roles in susceptibility to liver toxicity and disease. Hepatic miRNA expression was characterized at 2, 5, 6, 8, 15, 21, 52, 78, and 104 weeks of age in both sexes using Agilent 8x15k rat miRNA microarrays containing multiple probes for 677 unique miRNAs. Data processing, 75% normalization, and statistical analysis of microarray data were performed in SAS. Functional analysis (Ingenuity) was performed on select miRNAs exhibiting prominent age and sex expression differences. +
2017-02-19 | GSE65169 | GEO
Project description:Age as the primary rise factor could be play an important role in incidence and development of osteoarthritis. Several studies have confirmed some tissue specific microRNA were associated with development of osteoarthritis. But if age related microRNA or miRNA cluster would be involved in pivotal post-transcriptional gene regulation in osteoarthritis is unclear. In view of this, we have an idea that several age-related miRNAs would be screened from the rat knee cartilage at different development ages by miRNAs Microarray analysis. We used microarrays to detail the global programme of gene expression underlying the rat knee cartilage and identified distinct classes of age-related miRNAs during this process. The rat knee articular cartilage were selected at successive stages of the rat developmental for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of cartilage at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected cartilage according to the rat developmental stages, i.e. seven time-points: newborn (T0), childhood (T1), youth(T2), adult (T3), middle-aged (T4) early-stage elderly(T5) and latter-stage elderly(T6). The objective of the study is to identify miRNA profile of knee articular cartilage at different developmental ages in rats. Total RNA were extracted from the knee articular cartilage of Sprague-Dawley rats at postnatal day 0(T0), week1(T1), week 4(T2), mon3(T3), mon 6(T4), mon 12(T5), and mon 18(T6). The microRNA profile in the specimens was detected with the Affymetrix GeneChip® miRNA 3.0 Array.
2013-06-26 | E-GEOD-48266 | biostudies-arrayexpress
Project description:Purpose: The study aimed to determine the transcriptome profile of retinal miRNA in a Sprague Dawley (SD) rat model of oxygen-induced retinopathy Methods: The newborn rats in OIR group were subjected to daily cycles of 80% oxygen for 21 hours and room air for 3 hours in a customised chamber for 14 days (postnatal day 14, P14), then return to room air for 15 days (postnatal day 29, P29). The newborn rats in sham group were housed in room air for 14 days. Retinal miRNA expression profiles of OIR or sham rats at P14 or OIR rats at P29 were generated by deep sequencing, in triplicate, using Illumina Hiseq-2500 RNA-seq platform. Briefly, the sequence reads from all samples were analysed for overall quality, screened for the presence of any contaminants and trimmed accordingly. The cleaned sequence reads were then processed through the quantification modules miRDEEP2 ver2.0.0.7 pipeline for known miRNA expression profiling. Rat miRNAs from miRBASE release21 were used for mapping and quantification. Differential miRNA expression analysis was undertaken using voom bioconductor package (https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf). Results: A total of 465 miRNAs were identified in the rat retina. The miRNAs with significantly altered levels (P<0.05) were identified in OIR rats at P14 compared with the sham controls or OIR rats at P29. Among those altered miRNAs, seven miRNAs were down-regulated in OIR rats at P14 with Log2 (Fold Change) < -1 fold, and no miRNAs were up-regulated. Additionally, the expression of these down-regulated miRNAs in OIR rats at P14 was restored at P29 after they were exposed to room air. Conclusion: Our study represents the first detailed analysis of retinal miRNA expression profile in rat model of OIR by miRNA-NGS technology.
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Project description:Secondary hyperparathyroidism (SHP) is a common complication of chronic kidney disease (CKD) and correlates with morbidity and mortality. In this study we profiled microRNAs (miRNA) in parathyroids from different experimental SHP models and uremic patients and studied the function of specific miRNA using antagonizing oligonucleotides (anti-miRs). miRNA profiles established by small RNA deep sequencing showed that human, rat and mouse parathyroids share the same most abundant miRNAs. Principal component analyses clearly segregated parathyroids from SHP rats from normal rats, based on their miRNA expression profiles. Similar findings were observed in hyperplastic parathyroids from CKD patients compared to normal parathyroids from patients without kidney disease. We identifed specific parathyroid miRNAs that were dysregulated in all experimental SHP models studied. let-7i was decreased and miR-141 and miR-148a were increased in the parathyroids of rats with prolonged CKD induced by an 8 w adenine high phosphorus diet. Down-regulation of let-7 by anti-miRs increased PTH secretion in normal and in CKD rats, as well as in parathyroid organ cultures. Anti-miR-148 prevented the increase in serum PTH in CKD rats and decreased secreted PTH in parathyroid organ cultures. Our findings characterized parathyroid miRNA profiles and demonstrated conservation of the abundant miRNAs in different species. The evolutionary conservation of abundant miRNAs and their regulation in SHP suggest that miRNAs are important for parathyroid function and the development of SHP. Down-regulation of let-7 and miR-148 affects PTH secretion in vivo and in vitro, suggesting a role for these miRNAs in SHP. We propose that let-7 restrains while miR-148 promotes PTH secretion. In CKD, the decrease in parathyroid let-7 and the increase in miR-148 miRNAs may contribute to the development of SHP.
2017-03-21 | GSE79727 | GEO
Project description:MicroRNAs (miRNAs) are small (~22 nucleotide) noncoding RNAs that play pivotal roles in regulation of gene expression. The value of miRNAs as circulating biomarkers is now broadly recognized; such tissue-specific biomarkers can be used to monitor tissue injury and several pathophysiological conditions in organs. In addition, miRNA profiles of normal organs and tissues are important for obtaining a better understanding of the source of modulated miRNAs in blood and how those modulations reflect various physiological and toxicological conditions. This work was aimed at creating an miRNA atlas in rats, as part of a collaborative effort with the Toxicogenomics Informatics Project in Japan (TGP2). We analyzed genome-wide miRNA profiles of 55 different organs and tissues obtained from normal male rats using miRNA arrays. The work presented herein represents a comprehensive dataset derived from normal samples profiled in a single study. Here we present the whole dataset with miRNA profiles of multiple organs, as well as precise information on experimental procedures and organ-specific miRNAs identified in this dataset. miRNA expression in rat various organs was measured with or without saline perfusion. 3 animals were used.
2013-11-27 | E-GEOD-52754 | biostudies-arrayexpress
Project description:Background Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs. We confirmed the expression of 589 known miRNAs and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters. Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system. Small RNAs from 6 tissues were cloned and sequenced. Tissues included whole brain, liver, spleen, heart, testis, kidney. Tissues were sequenced from 2 rats: one BN-Lx rat and one SHR rat. For strain-specific miRNA expression we included 4 replicate whole livers, i.e. from 2 BN-Lx rats and 2 SHR rats.
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2015-08-04 | E-GEOD-71653 | biostudies-arrayexpress