Mus musculus strain:Ames dwarf
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA327085 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3727770.fastq.gz | Fastqsanger.gz | |||
| SRR3727780.fastq.gz | Fastqsanger.gz | |||
| SRR3729180.fastq.gz | Fastqsanger.gz | |||
| SRR3727771.fastq.gz | Fastqsanger.gz | |||
| SRR3729701.fastq.gz | Fastqsanger.gz |
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Project description:Gender-specific alterations in gene expression and loss of liver sexual dimorphism in the long-lived Ames dwarf mice.
2005-05-30 | E-MEXP-347 | biostudies-arrayexpress
Project description:Ovarian microRNA profile of long-living Ames dwarf mice during aging
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Project description:Recent evidence demonstrates that serum levels of specific small noncoding RNAs (sncRNAs) including miRNAs and 5’ tRNA halves significantly change with age. The ability of circulating sncRNAs to act as signaling molecules and regulate a broad spectrum of cellular functions implicates them as key players in the aging process. To discover circulating sncRNAs that impact aging in the long-lived Ames dwarf mice, we conducted deep sequencing of small RNAs extracted from serum of young and old mice. Our analysis showed genotype-specific changes in the circulating levels of 43 miRNAs and 19 5’ tRNA halves during aging [Genotype-by-Age interaction (GbA)]. GbA miRNAs showed four distinct expression patterns and significant over-targeting of transcripts involved in age-related processes. Functional enrichment analysis of putative miRNA targets highlighted cellular processes such as tumor suppression, anti-inflammatory response, and modulation of Wnt, insulin, mTOR, and MAPK signaling pathways, among others. The comparative analysis of circulating GbA miRNAs in Ames mice with circulating miRNAs modulated by calorie restriction (CR) in another long-lived mouse suggests CR-like and CR-independent mechanisms contributing to longevity in the Ames mouse. In conclusion, we showed for the first time a signature of circulating miRNAs and 5’-tRNA halves modulated by age in the long-lived Ames mouse.
2018-05-27 | GSE69274 | GEO
Project description:Female Ames dwarf mouse (df/df) with ad libitum access to water and standard pelleted food (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops. Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). Keywords = Ames dwarf Keywords = mouse Keywords = Affymetrix Keywords = caloric restriction Keywords: parallel sample
2005-01-10 | GSE1086 | GEO
Project description:To compare and contrast genetic signatures from livers of young and aged Ames dwarf mice with their wild type controls. Keywords: Time Course
2005-08-18 | GSE3150 | GEO
Project description:The aim of the current work was to evaluate the ovarian transcriptome in Ames dwarf (df/df) mice. df/df mice have a delayed ovarian aging compared to normal (N) mice. Although a high number of genes were differentially expressed during aging of N mice, only a small fraction of these changed with aging in df/df mice. These alterations involved more than 500 categorized biological processes. The majority of these biological processes, including inflammatory/immune responses, were up-regulated with aging in N mice, while old df/df mice were characterized by down-regulation of these same processes in comparison to age matched N mice. However, biological processes related to DNA damage and repairing were commonly down-regulated with aging in both genotypes. In conclusion, delayed ovarian aging in long-living df/df mice was associated with reduced expression of genes related to the inflammatory and immune responses.
2016-09-26 | GSE84078 | GEO
Project description:Female Ames dwarf mouse (df/df) with ad libitum access to water and fed 30% less of the standard pelleted diet with respect to the amount consumed by female ad libitum fed df/df mice (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops. Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). Keywords = Ames dwarf Keywords = mouse Keywords = Affymetrix Keywords = caloric restriction Keywords: parallel sample
2005-01-10 | GSE1087 | GEO
Project description:To compare and contrast genetic signatures from livers of young and aged Ames dwarf mice with their wild type controls. SUBMITTER_CITATION: W. H. Boylston, James H. DeFord, John Papaconstantinou (2006) Identification of longevity-associated genes in long-lived Snell and Ames dwarf mice Age 28:125-144 Experiment Overall Design: 25 micrograms of liver RNA was isolated from young (5 dwarfs, 5 wildtype), middle aged (5 dwarfs, 5 wild type) and aged (5 dwarf, 6 wild type) mice for use in hybridization of Affymetrix gene chips according to Affymetrix protocols.
2008-06-12 | E-GEOD-3150 | biostudies-arrayexpress
Project description:To compare and contrast genetic signatures from livers of young and aged Snell dwarf mice with their wild type controls. SUBMITTER_CITATION: W. H. Boylston, James H. DeFord, John Papaconstantinou (2006) Identification of longevity-associated genes in long-lived Snell and Ames dwarf mice Age 28:125-144 Experiment Overall Design: 25 micrograms of liver RNA was isolated from each of 6 aged (3 dwarf, 3 wild type) and 8 young (4 dwarf, 4 wild type) mice for use in hybridization of Affymetrix gene chips according to Affymetrix protocols.
2007-12-01 | E-GEOD-3129 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived Triticum aestivum transcriptome (RNA-seq) profiling methods and to evaluate genotypes associated with resistance against the Wheat dwarf virus. Methods: Triticum aestivum mRNA profiles of genotypes associated with resistance against the Wheat dwarf virus were generated by deep sequencing, in four replicates, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our study represents the first detailed analysis of Triticum aestivum transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA and miRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2023-04-04 | GSE192518 | GEO