GEO DataSets

(Submitter supplied) 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. more...

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18694

320 Samples

Download data: CSV, XLSX

(Submitter supplied) The study presents several novel findings that relate to the idea that alterations in DNA methylation occurs during aging and may be linked to senescent physiology, including a decline in circulating E2. In addition, the evidence has been provided that DNA methylation contributes to the closing of the critical window for E2 effects on synaptic function.

Organism:

Rattus norvegicus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23945

31 Samples

Download data: CSV

(Submitter supplied) Stem cells undergo differentiation in complex and dynamic environments wherein instructive signals fluctuate on various timescales. Thus, cells must be equipped to properly respond to the timing of signals, for example to distinguish sustained signaling from transient noise. However, how stem cells respond to dynamic variations in differentiation cues is not well characterized. Here, we use optogenetic activation of b-catenin signaling to probe the dynamic responses of differentiating adult neural stem cells (NSCs). more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

20 Samples

Download data: CSV

(Submitter supplied) Enzastaurin is a Protein Kinase C-β selective inhibitor that was developed to treat cancers. Protein Kinase C-β is an important enzyme for a variety of neuronal functions; in particular, previous rodent studies have reported deficits in spatial and fear-conditioned learning and memory with lower levels of Protein Kinase C-β. Due to Enzastaurin’s mechanism of action, the present study investigated the consequences of Enzastaurin exposure on learning and memory in 12-month-old Fischer-344 male rats. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

17 Samples

Download data: TXT

(Submitter supplied) The current study employed next generation RNA sequencing using two different platforms (Illumina and Ion Proton) to examine gene expression differences related to brain aging, cognitive decline, and hippocampus subregions (CA1, CA3, DG). Young and aged rats were trained on a spatial episodic memory task. The results describe regional differences in gene expression and point to regional differences in vulnerability to aging. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

102 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Rattus norvegicus; Macaca mulatta; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10558 GPL6885 GPL6101

64 Samples

Download data

(Submitter supplied) Aging is a complex phenomenon involving functional decline in multiple physiological systems. We focused on skeletal muscle to identify pathways that modulate function and healthspan by global expression profiles and specific mechanisms fundamental to aging processes. Our experimental design integrated comparative analysis of mice, rats, rhesus monkeys and humans and targeted three key time points during their lifespans. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL6101

15 Samples

Download data: TXT

(Submitter supplied) The carcinogenic effect of furan, a potent hepatotoxicant and rodent liver carcinogen, has been attributed to genotoxic and non-genotoxic, including epigenetic, changes in the liver; however, the mechanisms of the furan liver tumorigenicity are still unclear.  The goal of the present study was to investigate the role of transcriptomic and epigenetic events in the development of hepatic lesions in Fischer (F344) rats induced by furan treatment in a classic two-year rodent tumorigenicity bioassay.  Male F344 rats were distributed randomly into control and experimental groups.  Rats from the experimental groups were treated by gavage 5 days/week with either 0.92 or 2.0 mg furan/kg body weight (bw) in corn oil for 104 weeks.  Rats from control group received corn oil only.  High-throughput whole genome microarray analyses demonstrated distinctive dose-dependent alterations in gene expression in the furan-induced liver lesions.  A total of 2073 and 2422 genes was found to be differentially expressed in the furan-induced liver lesions in rats treated with 0.92 and 2.0 mg furan/kg bw, respectively, as compared to normal liver tissue.  Approximately 60% (1340) of the differentially expressed genes were common to both treatment groups.  In silico analysis of the common differentially expressed genes revealed the presence of CpG island in 51% (679) of the genes, suggesting that they may be epigenetically regulated.  Promoter methylation analysis of individual differentially expressed CpG island-containing genes demonstrated dose-dependent gene-specific methylation changes that were highly correlated with gene expression.  Our findings illustrate that gene-specific DNA methylation changes have functional consequences and may contribute to the development of furan-induced pathologic liver lesions.

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL13521

32 Samples

Download data: TXT

(Submitter supplied) Aristolochic Acid (AA), a natural component of Aristolochia plants found in a variety of herbal remedies and health supplements, is classified as a group 1 carcinogen by the International Agency for Research on Cancer. In order to search for miRNA regulation in AA-induced carcinogenesis, we treated rats with 10 mg/kg AA and vehicle control for 12 weeks and eight kidney samples (4 for the treatment and 4 for the control) were used for examining miRNA by deep sequencing.

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10287

8 Samples

Download data: TXT

(Submitter supplied) Furan is a heterocyclic organic compound produced in the chemical manufacturing industry and also found in a broad range of food products, including infant formulas and baby foods. Previous reports have indicated that the adverse biological effects of furan, including its liver tumorigenicity, may be associated with epigenetic abnormalities. In the present study we investigated the persistence of epigenetic alterations in rat liver. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL14797

8 Samples

Download data: TXT

(Submitter supplied) Vitamin D is an important calcium-regulating hormone with diverse functions in numerous tissues including the brain. Increasing evidence suggests that vitamin D may play a role in maintaining cognitive function and that vitamin D deficiency may accelerate age-related cognitive decline. Using aging rodents, we attempted to model the range of human serum vitamin D levels, from deficient to sufficient, to test whether vitamin D could preserve or improve cognitive function with aging. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS5345

Platform:

GPL6247

26 Samples

Download data: CEL

Analysis of hippocampus from F344 rats fed dietary supplement of cholecalciferol (vitamin D3) at doses of 10,000, 1000 and 100 IU/kg diet for 18 weeks. Results provide insight into molecular mechanisms underlying vitamin D-mediated synaptic function enhancement.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, transformed count, 3 dose sets

Platform:

GPL6247

Series:

GSE61326

26 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Rattus norvegicus; synthetic construct

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

15 related Platforms

4521 Samples

Download data: CEL, TXT

(Submitter supplied) In this study we employed the chronic unpredictable stress (CUS) rat model that leads to anxiety features comparable to humans and validated in several published reports as a well-characterized model of depression symptoms with high predictive validity. Cytokines and activated intracellular kinase levels were determined using high throughput multiplex assays. RNA from freshly isolated adipocytes was used to run whole genome expression microarray profiling in control and stressed rats. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL15084

12 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

320 Samples

Download data: TXT

(Submitter supplied) Aristolochic acid (AA) is an active component of herbal drugs derived from the Aristolochia species that have been used for medicinal purposes since antiquity. However, AA is genotoxic and induces tumors in animals and humans. AA induces mutations and tumors in the kidney but solely mutations in the liver. To evaluate whether miRNAs could indicate AA’s tissue-specific carcinogenicity and mutagenicity, we first conducted microarray analysis of miRNA expression in kidneys and livers of rats treated with a carcinogenic dose of AA. more...

Organism:

Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Non-coding RNA profiling by array

Platforms:

GPL17740 GPL10561

18 Samples

Download data: TXT

(Submitter supplied) Although glucocorticoids (GCs) are known to exert numerous effects in the hippocampus, their chronic regulatory functions remain poorly understood. Moreover, evidence is inconsistent regarding the longstanding hypothesis that chronic GC exposure promotes brain aging/Alzheimer's disease. Here, we adrenalectomized male F344 rats at 15-months-of-age, maintained them for 3 months with implanted corticosterone (CORT) pellets producing low or intermediate (glucocorticoid-receptor (GR)-activating) blood levels of CORT, and performed microarray/pathway analyses in hippocampal CA1. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS4757

Platform:

GPL85

39 Samples

Download data: CEL

Analysis of hippocampal CA1 from adrenalectomized F344 males maintained for 3 months with implanted corticosterone (CORT) pellets to produce low or intermediate (glucocorticoid receptor-activating) blood levels of CORT. Results provide insight into the effects of chronic CORT on the hippocampus.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, transformed count, 4 agent, 4 dose, 2 protocol sets

Platform:

GPL85

Series:

GSE37618

39 Samples

Download data: CEL

(Submitter supplied) Sleep deprivation (SD) in young adults is associated with metabolic, stress and cognitive responses that are also characteristic of brain aging. Given that sleep architecture changes with age, including increased fragmentation and decreased slow wave activity, it seems reasonable to investigate potential molecular relationships between SD and aging in brain tissue. Here, we tested the hypothesis that young rats exposed to 24 or 72 hour SD would respond with stress and aging-like shifts in brain hippocampal CA1 gene expression. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL85

69 Samples

Download data: CEL

(Submitter supplied) MicroRNAs (miRNAs) play an important role in carcinogenesis by regulating the protein translation from their targeted messenger RNAs (mRNA). Aristolochic Acid (AA) is a potent carcinogen that can induce kidney tumors in both human and experimental animals. Although the expression and roles of miRNAs have been extensively studied in cancer tissues or tissues treated by carcinogens, it is still unclear how the three levels of gene expression, including miRNA, mRNA and protein, are regulated and coordinated during the early stage of carcinogenesis. more...

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10287

8 Samples

Download data: TXT