Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA193226 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To address the issue of retention of somatic cell memory in iPSCs we compared methylation profiles of genetically matched human iPSCs derived from fibroblasts and blood. We were using the all-in-one type footprint free SeVdp-iPS system, for generation of uniform iPSC lines. Our results show that iPSC lines derived from the same donor are highly similar to each other. Experimental design: methylation profiles were assayed by Reduced Representation Bisulfite Sequencing (RRBS) for fibroblast-derived iPSC (N=8) and blood-derived iPSC (N=10) as well as isogenic parental fibroblasts and peripheral blood mononuclear cells (N=4 different donors: T14; T42; T53; T55). H9 human embryonic stem cell lines was used as control.
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Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
2010-09-25 | GSE24338 | GEO
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Project description:Summary To address the issue of retention of somatic cell memory in iPSCs we compared gene expressions of genetically matched human iPSCs derived from fibroblasts and blood. We were using the all-in-one type footprint free SeVdp-iPS system, for generation of uniform iPSC lines Our results show that iPSC lines derived from the same donor are highly similar to each other. Overal design Total RNA was extracted from fibroblasts derived iPSC (N=8) and blood derived iPSC (N=10) as well as parental fibroblasts and peripheral blood mononuclear cells (N=4 different donors: T14; T42; T53; T55). Total RNA was also extracted from spontaneously differentiated Embryonic bodies derived from fibroblasts derived iPSC (N=4) and blood derived iPSC (N=4) from four donors. RNA from control human embryonic stem cell lines (H9, and FES22) was used as control. Samples were run in two different batches (1 and 2).
2016-01-07 | E-MTAB-3825 | biostudies-arrayexpress
Project description:Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. It has been suggested that iPSC retain some tissue-specific memory whereas little is known about inter-individual epigenetic variation of iPSC clones. In this study we have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. Global DNA-methylation profiles of the initial MSC, MSC-derived iPSC (iP-MSC) and embryonic stem cells (ESC) were then compared using a high density DNA-methylation array covering more than 450,000 CpG sites. Overall, DNA-methylation patterns of iP-MSC and ESC were similar whereas some CpG sites revealed highly significant differences, which were not related to parental MSC. Furthermore, hypermethylation in iP-MSC versus ESC was particularly enriched in developmental genes as well as shore regions next to CpG islands indicating that these differences are not due to tissue-specific memory or random de novo methylation. Subsequently, we searched for CpG sites with donor-specific variation in MSC preparations. These “epigenetic fingerprints” were highly enriched in non-promoter regions and outside of CpG islands – and they were maintained upon reprogramming into iP-MSC. In conclusion, DNA methylation profiles of iP-MSC clones from the same donor were closely related despite heterogeneity of MSC. On the other hand, iP-MSC maintain donor-derived epigenetic differences. In the absence of isogenic controls for disease modeling applications, it would therefore be more appropriate to compare iPSC from different donors rather than a high number of different clones from the same patient. 16 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2013-01-09 | E-GEOD-34688 | biostudies-arrayexpress
Project description:Asthma is a chronic inflammatory airway disease characterized by airway inflammation and remodeling. The role of 15-oxo-5Z,8Z,11Z,13E-eicosatetraenoic acid (15-oxoETE), a 15-HETE metabolite catalyzed by 15-prostaglandin dehydrogenase (15-PGDH), has been relatively unexplored in asthma. In this study, we used RNA-seq to explore the effect of 15-KETE on the transcriptome of airway epithelial cells, aiming to identify its potential downstream targets and mechanisms of action.
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