E-GEOD-51518
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE51519PRJNA223347PRJNA223349PRJNA223350
PROVIDER: E-GEOD-51518 | ExpressionAtlas | 2025-01-24
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-51518-analysis-methods.tsv | Tabular | |||
| E-GEOD-51518-analytics.tsv | Tabular | |||
| E-GEOD-51518-analytics.tsv.undecorated | Tabular | |||
| E-GEOD-51518-analytics.tsv.undecorated.unrounded | Tabular | |||
| E-GEOD-51518-analytics.tsv.unrounded | Tabular |
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Similar Datasets
Project description:RNA-seq from primary skin fibroblasts, derived of matched pairs of middle and late donor age
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Project description:Chip-chip and MIRA-chip from primary skin fibroblasts, derived of matched pairs of early and late donor age
| PRJNA223349 | ENA
Project description:Aging signatures developed from a longitudinal study design are dominated by reduced transcription of genes involved in protein synthesis. Aging is a multifactorial process where the impact of singular components still remains unclear. Furthermore, previous studies were focused on measuring specific traits such as DNA -methylation and used categorical group-wise designs, unable to capture intra-individual signature changes. Here we have developed a new method for a longitudinal, age-related analysis combining the merits of a pair-wise design with the statistical power of gene set enrichment analysis. We present an integrated analysis, including transcriptional changes and genome-wide epigenetic changes in DNA- methylation, H3K4- and H3K27- histone methylation in promoter regions. We tested our method on a rare collection of paired skin fibroblast samples from male middle age to old age transitions and obtained functional, age-related clusters. By using a set of only ten individuals, we could demonstrate a high overlap of functional terms to previously established tissue-independent age signatures including extracellular matrix, apoptosis and oxidative stress. Importantly, we identify protein translation-related processes as the main cluster of age-driven, specific down regulation. H3K4me3, H3K27me3 and DNA- methylation longitudinal aging profiles from primary skin fibroblasts from matched pairs of early (E) and late (L) stages in life.
2014-10-23 | E-GEOD-51517 | biostudies-arrayexpress
Project description:Aging signatures developed from a longitudinal study design are dominated by reduced transcription of genes involved in protein synthesis Aging is a multifactorial process where the impact of singular components still remains unclear. Furthermore, previous studies were focused on measuring specific traits such as DNA -methylation and used categorical group-wise designs, unable to capture intra-individual signature changes. Here we have developed a new method for a longitudinal, age-related analysis combining the merits of a pair-wise design with the statistical power of gene set enrichment analysis. We present an integrated analysis, including transcriptional changes and genome-wide epigenetic changes in DNA- methylation, H3K4- and H3K27- histone methylation in promoter regions. We tested our method on a rare collection of paired skin fibroblast samples from male middle age to old age transitions and obtained functional, age-related clusters. By using a set of only ten individuals, we could demonstrate a high overlap of functional terms to previously established tissue-independent age signatures including extracellular matrix, apoptosis and oxidative stress. Importantly, we identify protein translation-related processes as the main cluster of age-driven, specific down regulation. Evaluation of transcriptional changes in matched sample pairs of primary skin fibroblasts from middle and old age.
2014-10-23 | E-GEOD-51518 | biostudies-arrayexpress
Project description:RNA-seq from control and macroH2A1-depleted IMR90 primary human lung fibroblasts
2025-01-24 | E-GEOD-54846 | ExpressionAtlas
Project description:Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). While these cultured fibroblasts were several generations removed from the primary tissue and morphologically indistinguishable, we found widespread epigenetic differences by sampling location at the single CpG (N=101,989), region (N=697), “block” (N=243), and global spatial scales suggesting a strong epigenetic memory of original fibroblast location. Furthermore, many of these epigenetic differences manifested in the transcriptome, particularly at the region-level. We further identified 7,265 CpGs and 11 regions showing significant epigenetic memory related to the age of the donor, as well as an overall increased epigenetic variability, preferentially in scalp-derived fibroblasts -83% of loci were more variable in scalp, hypothesized to result from cumulative exposure to environmental stimuli in the primary tissue. By integrating publicly available DNA methylation datasets on individual cell populations in blood and brain, we identified significantly increased inter-individual variability in our scalp- and other skin-derived fibroblasts on a similar scale as epigenetic differences between different lineages of blood cells. Lastly, these epigenetic differences did not appear to be driven by somatic mutation - while we identified 64 probable de-novo variants across the 11 subjects, there was no association between mutation burden and age of the donor (p=0.71). These results depict a strong component of epigenetic memory in cell culture from primary tissue, even after several generations of daughter cells, related to cell state and donor age.
2016-01-23 | GSE77135 | GEO
Project description:Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). While these cultured fibroblasts were several generations removed from the primary tissue and morphologically indistinguishable, we found widespread epigenetic differences by sampling location at the single CpG (N=101,989), region (N=697), “block” (N=243), and global spatial scales suggesting a strong epigenetic memory of original fibroblast location. Furthermore, many of these epigenetic differences manifested in the transcriptome, particularly at the region-level. We further identified 7,265 CpGs and 11 regions showing significant epigenetic memory related to the age of the donor, as well as an overall increased epigenetic variability, preferentially in scalp-derived fibroblasts -83% of loci were more variable in scalp, hypothesized to result from cumulative exposure to environmental stimuli in the primary tissue. By integrating publicly available DNA methylation datasets on individual cell populations in blood and brain, we identified significantly increased inter-individual variability in our scalp- and other skin-derived fibroblasts on a similar scale as epigenetic differences between different lineages of blood cells. Lastly, these epigenetic differences did not appear to be driven by somatic mutation - while we identified 64 probable de-novo variants across the 11 subjects, there was no association between mutation burden and age of the donor (p=0.71). These results depict a strong component of epigenetic memory in cell culture from primary tissue, even after several generations of daughter cells, related to cell state and donor age.
2016-01-23 | GSE77131 | GEO
Project description:In the project “A Dual-Acting Nitric Oxide Donor and Phosphodiesterase 5 Inhibitor Activates Autophagy in Primary Skin Fibroblasts» by Esther Martínez-Martínez and Joern Dengjel, we performed expression proteomics analyzing the response of normal human fibroblasts (NHF) isolated from healthy skin to the drug TOP-N53.
2022-06-25 | PXD032893 | Pride
Project description:Background: Skin homeostasis is mediated by dermal fibroblasts and is affected by aging. Although age-related heterogeneity in fibroblasts has been reported, the effects of donor and species on this heterogeneity are unclear. Methods: To analyze age-related transcriptomic changes in human dermal fibroblasts, single-cell RNA sequencing was performed on dermal fibroblasts (ASF-4 cells) collected from the inner forearm of a volunteer over three decades. Results: Four main cell subpopulations changed with donor age and showed proliferative, homeostasis, fibrotic, and senescence functional annotations. The downregulation of the expression of genes encoding key extracellular matrix production and mechanotransduction components decreased with donor age. Interestingly, dermal fibroblasts have two putative differentiation pathways: one that involves the acquisition of senescent properties and the acquisition of fibrotic properties without the suppression of proliferation. Aging induced fibroblast differentiation in a manner involving the acquisition of senescent properties. Conclusion:Reconciling the various aspects of fibroblast heterogeneity may provide insight into the mechanisms underlying human skin aging and associated phenomena, including wrinkles, sagging, delayed wound healing, and suppressed scar formation.
2023-09-21 | GSE203034 | GEO
Project description:Extrinsic skin ageing converges on the dermis, a post-mitotic tissue compartment consisting of extracellular matrix and long-lived fibroblasts prone to damage accumulation and maladaptation. Aged human fibroblasts exhibit mitochondrial and nuclear dysfunctions, but it is unclear whether these are cause or consequence of ageing. We report on a systematic study of human dermal fibroblasts retrieved from female donors aged 20-67 years and analyzed in primary culture at low population doubling precluding replicative senescence. Genome-wide array analysis failed to detect significant (>2-fold) age-related expression changes for individual genes, but gene set enrichment analysis revealed down regulation of many genes involved in mitochondrial metabolism and respiratory electron transport, extracellular matrix maintenance, cell cycle progression and protein translation. Consistent with these changes, mitochondrial content, respiratory function and cell proliferation declined with donor age. This was associated with inadequate nuclear mito-biogenesis, hypo- phosphorylation of AMP-dependent protein kinase alpha and upregulation of the alpha2-isoform, suggesting that inadequate mito-nuclear signalling could be the leading event entailing decreased expression of mitochondrial genes and compensatory down regulation of proliferation and protein synthesis. The comparatively few genes exhibiting age-associated up regulation were associate with cholesterol metabolism, immune reactions and mRNA processing, possibly also reflecting adaptation to inadequate mitochondrial function. Donors: 15 human female donors included in the study were aged 20, 21, 23, 26, 26, 40, 41, 42, 43, 49, 60, 62, 63, 64 and 67 years, thus covering the age spectrum 20 – 67 years and providing five biological replicates for each of the age groups “young” (20-30 years), “middle” (40-50 years) and “old” (60-70 years). Human dermal fibroblasts were isolated from skin specimen removed in the course of cosmetic surgery from the bottom side of female breast. Isolation and primary culture of the cells followed published procedures (Tigges and others 2013). Cells were not expanded beyond 12 population doublings, while replicative cell cycle arrest was determined to not occur before 40 population doublings.
2014-04-08 | E-GEOD-55118 | biostudies-arrayexpress