Effect of ERI1 deficiency on gene expression during chondrogenic differentiation of human iPSCs
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE206412 | GEO | 2023/07/01
REPOSITORIES: GEO
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Project description:Pluripotent cells can be derived from somatic cells by either overexpression of defined transcription factors (resulting in induced pluripotent stem cells (iPSCs)) or by nuclear transfer or cloning (resulting in NT-ESCs). To determine whether cloning further reprograms iPSCs, we used iPSCs as donor cells in nuclear transfer experiments. An iPSC clone derived from tail-tip fibroblasts using adenoviral vectors was used as donor cell in nuclear transfer experiments. RNA was isolated from both parental iPSC clone and derivative NT-ESCs lines and analyzed.
2010-05-27 | E-GEOD-20575 | biostudies-arrayexpress
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.
2016-08-18 | E-MTAB-3859 | biostudies-arrayexpress
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:PURPOSE: The goal of this study was to develop a lot release assay for iPSC residuals following directed differentiation of iPSCs to retinal pigment epithelial (RPE) cells. METHODS: RNA Sequencing (RNA Seq) of iPSCs and RPE derived from them was used to identify pluripotency markers downregulated in RPE cells. Quantitative real time PCR (qPCR) was then applied to assess iPSC residuals in iPSC-derived RPE. The limit of detection (LOD) of the assay was determined by performing spike-in assays with known quantities of iPSCs serially diluted into an RPE suspension. RESULTS: ZSCAN10 and Lin28a were among 8 pluripotency markers identified by RNA Seq as downregulated in RPE. Based on copy number and expression of pseudogenes and lncRNAs ZSCAN10 and Lin28a were chosen for use in qPCR assays for residual iPSCs. Reverse transcription PCR indicated generally uniform expression of ZSCAN10 and Lin28a in 21 clones derived from 8 iPSC donors with no expression of either in RPE cells derived from 5 donor lines. Based on qPCR, ZSCAN10 and Lin28a expression in iPSCs was generally uniform. The LOD for ZSCAN10 and Lin28a in qPCR assays was determined using spike in assays of RPE derived from 2 iPSC lines. Analysis of DDCt found the limit of detection to be <0.01% of cells, equivalent to <1 iPSC / 10,000 RPE cells in both iPSC lines. CONCLUSIONS: qPCR for ZSCAN10 and Lin28a detects <1 in 10,000 residual iPSCs in a population of iPSC-derived RPE providing an adequate LOD of iPSC residuals for lot release testing.
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Project description:Effect of ERI1 deficiency on gene expression during chondrogenic differentiation of human iPSCs
| PRJNA850508 | ENA
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2011-05-31 | E-GEOD-24705 | biostudies-arrayexpress
Project description:Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. Here we investigate the use of iPSCs and iPSC-derived cells to study the impact of genetic variation across different cell types and as models for the genetics of complex disease. We established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring RNA, chromatin accessibility and DNA methylation. Regulatory variation between individuals is lower in iPSCs than in the differentiated cell types, consistent with the intuition that developmental processes are generally canalized. While most cell-type- specific regulatory effects lie in chromatin that is open only in the affected cell-types, we find that 20% of cell-type specific effects are in shared open chromatin. Finally, we developed deep neural network models to predict open chromatin regions in these cell types from DNA sequence alone and were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on tissue-specific chromatin accessibility. Our results provide a framework for using iPSC technology to study regulatory variation in cell types that are otherwise inaccessible. Keywords: Expression profiling by high throughput sequencing
2017-12-05 | GSE107654 | GEO
Project description:The integration of cell metabolism with signalling pathways, transcription factor networks and epigenetic mediators is critical in coordinating molecular and cellular events during embryogenesis. Induced pluripotent stem cells (IPSCs) are an established model for embryogenesis, germ layer specification and cell lineage differentiation, advancing the study of human embryonic development and the translation of innovations in drug discovery, disease modelling and cell-based therapies. The metabolic regulation of IPSC pluripotency is mediated by balancing glycolysis and oxidative phosphorylation, but there is a paucity of data regarding the influence of individual metabolite changes during cell lineage differentiation. We used <sup>1</sup>H NMR metabolite fingerprinting and footprinting to monitor metabolite levels as IPSCs are directed in a three-stage protocol through primitive streak/mesendoderm, mesoderm and chondrogenic populations. Metabolite changes were associated with central metabolism, with aerobic glycolysis predominant in IPSC, elevated oxidative phosphorylation during differentiation and fatty acid oxidation and ketone body use in chondrogenic cells. Metabolites were also implicated in the epigenetic regulation of pluripotency, cell signalling and biosynthetic pathways. Our results show that <sup>1</sup>H NMR metabolomics is an effective tool for monitoring metabolite changes during the differentiation of pluripotent cells with implications on optimising media and environmental parameters for the study of embryogenesis and translational applications.
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Project description:Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. An alternative to the LCL model is the induced pluripotent stem cell (iPSC) system, which carries the potential to model tissue-specific physiology through the use of differentiation protocols. Still, existing LCL banks represent an important source of starting material for iPSC generation, and it is possible that the disruptions in gene regulation associated with long-term LCL maintenance could persist through the reprogramming process. To address this concern, we studied the effect of reprogramming mature LCLs to iPSCs on the ensuing gene expression patterns within and between six unrelated donor individuals. We show that the reprogramming process results in a recovery of donor-specific gene regulatory signatures. Since environmental contributions are unlikely to be a source of individual variation in our system of highly passaged cultured cell lines, our observations suggest that the effect of genotype on gene regulation is more pronounced in the iPSCs than in the LCL precursors. Our observations indicate that iPSCs can be a powerful model system for studies of phenotypic variation across individuals in general, and the genetic association with variation in gene regulation in particular. We further conclude that LCLs are an appropriate starting material for iPSC generation. Whole genome gene expression data was collected for 34 samples including 17 iPSC lines and 17 LCL lines on the Illumina HT-12 v4 Expression BeadChip array platform. Three biological replicates of each individual were included in the study, except for one individual for which only two replicates were obtained.
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