Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deep sequencing of small RNAs from Mouse brain during aging

ABSTRACT: MicroRNAs (miRNAs) are endogenous small RNA molecules that regulate gene expression post-transcriptionally. Work in Caenorhabditis elegans has shown that specific miRNAs function in lifespan regulation and in a variety of age-associated pathways, but the roles of miRNAs in the aging of vertebrates are not well understood. We examined the expression of small RNAs in whole brains of young and old mice by deep sequencing and report here on the expression of 233 known miRNAs and identification of 41 novel miRNAs. Of these miRNAs, 75 known and 18 novel miRNAs exhibit greater than 2.0-fold expression changes. The majority of expressed miRNAs in our study decline in relative abundance in the aged brain, in agreement with trends observed in other miRNA studies in aging tissues and organisms. Target prediction analysis suggests that many of our novel aging-associated miRNAs target genes in the insulin signaling pathway, a central node of aging-associated genetic networks. These novel miRNAs may thereby regulate aging-related functions in the brain. Since mouse miRNAs are conserved in humans, the aging-affected brain miRNAs we report here may represent novel regulatory genes that function during aging in the human brain.

ORGANISM(S): Mus musculus

PROVIDER: GSE34393 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA149571

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Deep sequencing of small RNAs from Mouse brain during aging

Project description:MicroRNAs (miRNAs) are endogenous small RNA molecules that regulate gene expression post-transcriptionally. Work in Caenorhabditis elegans has shown that specific miRNAs function in lifespan regulation and in a variety of age-associated pathways, but the roles of miRNAs in the aging of vertebrates are not well understood. We examined the expression of small RNAs in whole brains of young and old mice by deep sequencing and report here on the expression of 233 known miRNAs and identification of 41 novel miRNAs. Of these miRNAs, 75 known and 18 novel miRNAs exhibit greater than 2.0-fold expression changes. The majority of expressed miRNAs in our study decline in relative abundance in the aged brain, in agreement with trends observed in other miRNA studies in aging tissues and organisms. Target prediction analysis suggests that many of our novel aging-associated miRNAs target genes in the insulin signaling pathway, a central node of aging-associated genetic networks. These novel miRNAs may thereby regulate aging-related functions in the brain. Since mouse miRNAs are conserved in humans, the aging-affected brain miRNAs we report here may represent novel regulatory genes that function during aging in the human brain. 2 samples examined: Mouse brain from two young (5 months) and two old animals (24-25 months).

2012-05-31 | E-GEOD-34393 | biostudies-arrayexpress

Deep sequencing of small RNAs from C. elegans during aging

Project description:Aging is under genetic control in C. elegans but the mechanisms of lifespan regulation are not completely known. MicroRNAs (miRNAs) regulate various aspects of development and metabolism and one miRNA has been previously implicated in lifespan. Here we show that multiple miRNAs change expression in C. elegans aging, including novel miRNAs, and that mutations in several of the most up-regulated miRNAs lead to lifespan defects. Some act to promote normal lifespan and stress resistance while others inhibit these phenomena. We find that these miRNAs genetically interact with genes in the DNA damage checkpoint response pathway and in the insulin signaling pathway. Our findings reveal that miRNAs both positively and negatively influence lifespan. Since several miRNAs up-regulated during aging regulate genes in conserved pathways of aging and thereby influence lifespan in C. elegans, we propose that miRNAs may play important roles in stress response and aging of more complex organisms. 4 sample examined: Wild-type (N2) and long-lived daf-2(e1379) animals at days 0 and 10 of adulthood

2011-01-01 | E-GEOD-24510 | biostudies-arrayexpress

Vastus lateralis muscle aging

Project description:Development of a method to identify age-regulated expression trends in skeletql muscles and study the underlying molecular processes of the age_associated progressive changes in skeletal muscles. See abstract from associated manuscript belowÂ : Aging is characterized by progressive tissue degeneration and it is associated with genome-wide changes of mRNA expression profiles. Therefore, it is expected that age-regulated changes in expression profiles could describe the process of aging. We have developed a robust and unbiased methodology to identify age-regulated expression trends in cross-sectional data sets from healthy donors. Our analysis in four different tissues reveals that in brain cortex and Vastus lateralis muscles, two major age-associated expression inclinations were found, one during midlife and one in elderly. In kidney medulla and cortex, however, transcriptional changes were found only in elderly. In concurrence with increased degeneration in aged tissue, the elderly-associated expression changes are predominantly downwards. Our results suggest that a non-linear trend describes the aging process, and can be the result of inclinations of gene expression at two distinct age-positions affecting different molecular and cellular processes. RNA was extracted from vastus lateralis muscles. cDNA synthesis and labeling were preformed with the Illumina cDNA labeling kit.

2012-12-03 | E-GEOD-40645 | biostudies-arrayexpress

Deep sequencing of small RNAs from C. elegans during aging

2011-01-01 | GSE24510 | GEO

Vastus lateralis muscle aging

Project description:Development of a method to identify age-regulated expression trends in skeletql muscles and study the underlying molecular processes of the age_associated progressive changes in skeletal muscles. See abstract from associated manuscript below : Aging is characterized by progressive tissue degeneration and it is associated with genome-wide changes of mRNA expression profiles. Therefore, it is expected that age-regulated changes in expression profiles could describe the process of aging. We have developed a robust and unbiased methodology to identify age-regulated expression trends in cross-sectional data sets from healthy donors. Our analysis in four different tissues reveals that in brain cortex and Vastus lateralis muscles, two major age-associated expression inclinations were found, one during midlife and one in elderly. In kidney medulla and cortex, however, transcriptional changes were found only in elderly. In concurrence with increased degeneration in aged tissue, the elderly-associated expression changes are predominantly downwards. Our results suggest that a non-linear trend describes the aging process, and can be the result of inclinations of gene expression at two distinct age-positions affecting different molecular and cellular processes.

2012-12-03 | GSE40645 | GEO

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Project description:The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish, substantially less microRNAs have been discovered in zebrafish compared to human (Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In brain, gut and liver sequencing was done in male and female separately. Majority of the sequenced reads (16-62%) mapped to known miRNAs, with the exception of ovary (5.7%) and testis (7.8%). Using the miRNA discovery tool (miRDeep2), we discovered novel miRNAs from the un-annotated reads that ranged from 7.6 to 23.0%, with exceptions of ovary (51.4%) and testis (55.2%). The prediction tool identified a total of 459 novel pre-miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated (22) and sex associated (34) miRNAs, respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further, we have discovered 459 novel pre-miRNAs (~30% seed homology to human miRNA) as a genomic resource which can facilitate further investigations to understand miRNA-mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Known miRNA profiling, novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish (in triplicate) was carried out using the Illumina HiSeq 2000 platform.

2015-10-16 | E-GEOD-57169 | biostudies-arrayexpress

ChIP-Seq of human endogenous small RNAs associated to Argonaute 1 and 2

Project description:Small non-coding RNAs function in concert with Argonaute (Ago) proteins to regulate gene expression at the level of transcription, mRNA stability or translation. Ago proteins bind small RNAs and form the core of silencing complexes. Here we report the analysis of small RNAs associated with human Ago1 and Ago2 revealed by immunoprecipitation and deep sequencing. Among the reads we find small RNAs originating from the small nucleolar RNA (snoRNA) ACA45. Moreover, processing of ACA45 requires Dicer activity but is independent of Drosha/DGCR8. Using bio-informatic prediction algorithms and luciferase reporter assays, we uncover the mediator subunit CDC2L6 as one potential mRNA target of ACA45 small RNAs suggesting a role for ACA45 processing products in post-transcriptional gene silencing. We further identify a number of human snoRNAs with microRNA (miRNA)- like processing signatures. We have therefore identified a novel class of small RNAs in human cells that originate from snoRNAs and can function like miRNAs. Two samples examined. Small RNAs associated to human Argonaute 1 and human Argonaute 2

2008-11-20 | E-GEOD-13370 | biostudies-arrayexpress

Discovery of microRNAs and other small RNAs in solid human tumors: sequencing

Project description:MicroRNAs (miRNAs) are ~22 nucleotide-long, non-coding RNAs that regulate gene silencing. It is known that many human miRNAs are deregulated in numerous types of tumors. Here we report the sequencing of small RNAs from 23 breast, bladder, colon, and lung tumor samples using high-throughput sequencing. We identified 49 novel miRNA and miRNA-like small RNAs. We further validated the expression of 10 novel small RNAs in 31 different types of blood, normal and tumor tissue samples using two independent platforms, namely microarray and RT-PCR. Some of the novel sequences show a large difference in expression between tumor and tumor-adjacent tissues, between different tumor stages, or between different tumor types. We also report the identification of novel small RNA classes in human: highly expressed small RNA derived from Y-RNA and endogenous siRNA. Finally, we identified dozens of new miRNA sequence variants that demonstrate the existence of miRNA-related SNP or post-transcriptional modifications. Our work extends the current knowledge of the tumor small RNA transcriptome and provides novel candidates for molecular biomarkers and drug targets.

2010-05-20 | GSE20417 | GEO

Discovery of microRNAs and other small RNAs in solid human tumors: expression

Project description:MicroRNAs (miRNAs) are ~22 nucleotide-long, non-coding RNAs that regulate gene silencing. It is known that many human miRNAs are deregulated in numerous types of tumors. Here we report the sequencing of small RNAs from 23 breast, bladder, colon, and lung tumor samples using high-throughput sequencing. We identified 49 novel miRNA and miRNA-like small RNAs. We further validated the expression of 10 novel small RNAs in 31 different types of blood, and normal and tumor tissue samples using two independent platforms, namely microarray and RT-PCR. Some of the novel sequences show a large difference in expression between tumor and tumor-adjacent tissues, between different tumor stages, or between different tumor types. We also report the identification of novel small RNA classes in human: highly expressed small RNA derived from Y-RNA and endogenous siRNA. Finally, we identified dozens of new miRNA sequence variants that demonstrate the existence of miRNA-related SNP or post-transcriptional modifications. Our work extends the current knowledge of the tumor small RNA transcriptome and provides novel candidates for molecular biomarkers and drug targets.

2010-05-20 | GSE20414 | GEO

Genome-wide maps of AGO1-bound small RNA in Arabidopsis leaves

Project description:We report flg22 regulate the accumulation of AGO1-bound small RNA in arabidopsis. We find that a number of miRNAs are up- or down-regulated by flg22, a well-studied PAMP. Examination of AGO1-bound small RNAs with or without flg22 treatment.

2010-02-25 | E-GEOD-20448 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data