Transcriptome expression study with chronological aging in human hippocampus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA828461 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In our study, we performed a transcriptomic analysis from hippocampal samples from human individuals of different ages. We identified a set of genes that were differentially expressed in aged samples. Moreover, we revealed a subset of genes whose expression correlated with chronological aging. Analysis in a validation cohort confirmed some genes having negative correlation with age. Additional immunohistochemistry in another validation cohort confirmed transcriptomic results. In summary, these results identify putative biomarkers and regulators of brain aging.
2024-08-21 | GSE201118 | GEO
Project description:We analyzed transcriptomic features associated with physiological and chronological aging using Caenorhabditis elegans as a model.
2022-10-04 | GSE190068 | GEO
Project description:To gain an understanding of processes that underlie chronological aging in this dinoflagellate, a microarray study was carried out to identify changes in the global transcriptome that accompany the entry and maintenance of stationary phase up to the onset of cell death. The transcriptome of K. brevis was assayed using a custom 10,263 feature oligonucleotide microarray from mid-logarithmic growth to the onset of culture demise. A total of 2,958 (29%) features were differentially expressed, with the mid-stationary phase timepoint demonstrating peak changes in expression. Gene ontology enrichment analyses identified a significant shift in transcripts involved in energy acquisition, ribosome biogenesis, gene expression, stress adaptation, calcium signaling, and putative brevetoxin biosynthesis. The extensive remodeling of the transcriptome observed in the transition into a quiescent non-dividing phase appears to be indicative of a global shift in the metabolic and signaling requirements and provides the basis from which to understand the process of chronological aging in a dinoflagellate. Twenty seven 900ml batch cultures of K. brevis were inoculated at a starting concentration of approximately 1000 cells/ml from mid-logarithmic stage starter cultures on day 0. Triplicate cultures were harvested every other day from day 2 to 18 and total RNA was extracted. One color arrays were then run on all biological replicates (n=3 at each timepoint) for days 4, 6, 10, 14 and 18.
2012-01-01 | E-GEOD-31913 | biostudies-arrayexpress
Project description:Skeletal muscle is a post-mitotic tissue that exhibits an extremely low turnover in the absence of disease or injury. At the same time, muscle possesses remarkable regenerative capacity mediated by satellite cells (SCs) that reside in close association with individual myofibers, underneath the fiber’s basal lamina. Consistent with the low turnover of the muscle, SCs in adult animals are mitotically quiescent and therefore provide an excellent model to study stem cell quiescence. As an organism grows older, the resident stem cells are exposed to a deteriorating environment and experience chronological aging. In stem cells with high turnover, the effects of chronological aging are superimposed upon the effects of the replicative aging that results from DNA replication and cell division. On the contrary, SCs experience minimal replicative aging due to their low turnover. They are thus a good model to study the consequence of chronological aging of quiescent stem cells. We performed microarray analysis of quiescent and activated SCs from both young and aged mice to understand the global gene expression profile underlying stem cell properties such as quiecence and self-renewal, and to understand how the transcriptome of a quiescent stem cell pouplation changes with age. VCAM+/CD31-/CD45-/Sca1- quiescent satellite cells (QSCs) were isolated by FACS from hindlimb muscle of uninjured 2-3- or 22-24-month old mice. Activated satellite cells (ASCs) were isolated from hindlimb muscles of BaCl2-injured mice of the same age 36, 60 and 84 hours after injury using the same cell surface marker combination. YFP-expressing cells were isolated from 2-3-month old Pax7CreER/+; ROSA26eYFP/+ mice in which satellite cells are labeled geneticall by YFP expression. Total RNA was extracted from cells with the Trizol reagent according to manufacturer's instructions. RNA was then processed and assayed with Affymetrix Mouse Gene 1.0 ST arrays.
2013-05-23 | E-GEOD-47177 | biostudies-arrayexpress
Project description:Skeletal muscle is a post-mitotic tissue that exhibits an extremely low turnover in the absence of disease or injury. At the same time, muscle possesses remarkable regenerative capacity mediated by satellite cells (SCs) that reside in close association with individual myofibers, underneath the fiber’s basal lamina. Consistent with the low turnover of the muscle, SCs in adult animals are mitotically quiescent and therefore provide an excellent model to study stem cell quiescence. As an organism grows older, the resident stem cells are exposed to a deteriorating environment and experience chronological aging. In stem cells with high turnover, the effects of chronological aging are superimposed upon the effects of the replicative aging that results from DNA replication and cell division. On the contrary, SCs experience minimal replicative aging due to their low turnover. They are thus a good model to study the consequence of chronological aging of quiescent stem cells. We performed microarray analysis of quiescent and activated SCs from both young and aged mice to understand the global gene expression profile underlying stem cell properties such as quiecence and self-renewal, and to understand how the transcriptome of a quiescent stem cell pouplation changes with age.
2013-05-23 | GSE47177 | GEO
Project description:Skeletal muscle is a post-mitotic tissue that exhibits an extremely low turnover in the absence of disease or injury. At the same time, muscle possesses remarkable regenerative capacity mediated by satellite cells (SCs) that reside in close association with individual myofibers, underneath the fiberM-bM-^@M-^Ys basal lamina. Consistent with the low turnover of the muscle, SCs in adult animals are mitotically quiescent and therefore provide an excellent model to study stem cell quiescence. As an organism grows older, the resident stem cells are exposed to a deteriorating environment and experience chronological aging. In stem cells with high turnover, the effects of chronological aging are superimposed upon the effects of the replicative aging that results from DNA replication and cell division. On the contrary, SCs experience minimal replicative aging due to their low turnover. They are thus a good model to study the consequence of chronological aging of quiescent stem cells. We have developed an isolation protocol to selectively enrich SCs by FACS from adult mice and applied the ChIP-seq technology to obtain H3K4me3, H3K27me3 and H3K36me3 from quiescent and activated SCs from young mice and from quiescent SCs from old mice. Our analysis aims to understand the chromatin features underlying stem cell properties such as quiecence and lineage-potency, and to understand how the chromatin structure of a quiescent stem cell pouplation changes with age. VCAM+/CD31-/CD45-/Sca1- quiescent satellite cells (QSCs) were isolated by FACS from hindlimb muscle of uninjured 2-3- or 22-24-month old mice and processed for ChIP-seq.
2013-08-13 | E-GEOD-47362 | biostudies-arrayexpress
Project description:To gain an understanding of processes that underlie chronological aging in this dinoflagellate, a microarray study was carried out to identify changes in the global transcriptome that accompany the entry and maintenance of stationary phase up to the onset of cell death. The transcriptome of K. brevis was assayed using a custom 10,263 feature oligonucleotide microarray from mid-logarithmic growth to the onset of culture demise. A total of 2,958 (29%) features were differentially expressed, with the mid-stationary phase timepoint demonstrating peak changes in expression. Gene ontology enrichment analyses identified a significant shift in transcripts involved in energy acquisition, ribosome biogenesis, gene expression, stress adaptation, calcium signaling, and putative brevetoxin biosynthesis. The extensive remodeling of the transcriptome observed in the transition into a quiescent non-dividing phase appears to be indicative of a global shift in the metabolic and signaling requirements and provides the basis from which to understand the process of chronological aging in a dinoflagellate.
2012-01-01 | GSE31913 | GEO
Project description:Histone modification affects life span in various organisms. The loss of Histone H3K36 methylation can shorten replicative life span in Saccharomyces cerevisiae. However, budding yeast, as a model organism for aging research, has replicative life span (RLS) and chronological life span (CLS). In this study, we showed that the loss of Histone H3K36 methylation can shorten CLS in Saccharomyces cerevisiae. We identified Ubc3/Bre1 mediates polyubiquitination of Set2 K25 and K530 at log phase and stationary phase, and Bre1 interacts with Ubc3 and Rad6 simultaneously. BRE1 knockout can stabilize Set2 protein to maintain H3K36me3 and regulate the transcription of aging related genes, such as DSE1/DSE2/SUN4/EGT2/SCW11. We also proved that Gcn5-mediated Set2 acetylation regulates Set2 protein stability and chronological aging. Altogether, our study showed that knockout of BRE1 and GCN5 regulate Set2 protein level by mediating the polyubiquitination of Set2 to influence the level of H3K36me3 and the transcription level of aging related genes enriched by H3K36me3, thereby extending the chronological life span.
2023-09-29 | GSE221025 | GEO
Project description:Histone modification affects life span in various organisms. The loss of Histone H3K36 methylation can shorten replicative life span in Saccharomyces cerevisiae. However, budding yeast, as a model organism for aging research, has replicative life span (RLS) and chronological life span (CLS). In this study, we showed that the loss of Histone H3K36 methylation can shorten CLS in Saccharomyces cerevisiae. We identified Ubc3/Bre1 mediates polyubiquitination of Set2 K25 and K530 at log phase and stationary phase, and Bre1 interacts with Ubc3 and Rad6 simultaneously. BRE1 knockout can stabilize Set2 protein to maintain H3K36me3 and regulate the transcription of aging related genes, such as DSE1/DSE2/SUN4/EGT2/SCW11. We also proved that Gcn5-mediated Set2 acetylation regulates Set2 protein stability and chronological aging. Altogether, our study showed that knockout of BRE1 and GCN5 regulate Set2 protein level by mediating the polyubiquitination of Set2 to influence the level of H3K36me3 and the transcription level of aging related genes enriched by H3K36me3, thereby extending the chronological life span.
2023-09-29 | GSE221024 | GEO
Project description:Aging is a complex process characterized by a progressive decline in physiological integrity that leads to impaired cellular and tissue function. Adult stem cells play a critical role in organismal health and aging. Their age-related deterioration contributes to a reduced homeostatic and regenerative capacity. Notably, most studies of stem cell aging focus on the mechanisms of replicative aging in stem cells with high cellular turnover. Yet, the therapeutic potential of stem cells with low cellular turnover, such as adipose-derived stem cells (ASC), is increasingly recognized as potentially superior. The mechanism of aging in low turnover stem cells is thought to differ from those with high turnover and to more closely reflect chronological aging. The latter, however, is exceedingly difficult to study in slowly replicating primary human stem cells and thus remains poorly understood. Here, we employ our unique model of chronological aging in primary human ASCs to examine genome-wide transcriptional networks in early chronological aging using RNA-seq analyses. Our findings demonstrate that the transcriptome of aging ASCs is more stable than that of age-matched fibroblasts. Limited transcriptional modifications in aging ASCs reveal more active transcriptional profiles of cell cycle genes and translation initiation genes when compared with aging differentiated cells. Accordingly, nascent protein synthesis, measured by incorporation of op-puromycin, is increased in ASCs from older individuals, concurrent with a decreased phosphorylation at ser-51 of eIF2, a mechanism of inhibiting translation initiation. A shortened G1 phase observed in the old ASCs could be linked to the increased protein synthesis activity, potentially resulting in more active cell proliferation. This effect, however, is not detected in aging fibroblasts. The altered regulation of cell cycle in aging ASCs could allow a more active cell proliferation to meet an increase demand to preserve tissue and organ functions. These observations are consistent with data supporting the maintenance of ASC integrity in aging human adipose tissue and reveal early chronological aging mechanisms in ASCs that are inherently different from other cell types.
2017-02-24 | GSE86244 | GEO