Mus musculus
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ABSTRACT:
PROVIDER: PRJNA359213 | ENA |
REPOSITORIES: ENA
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Project description:Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells
| PRJNA359211 | ENA
Project description:Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells [RNA-seq]
| PRJNA359212 | ENA
Project description:Here we performed genome-wide RNA-seq and Reduced Representation Bisulfite Sequencing (RRBS-seq) in isogenic human induced pluripotent stem cells (iPSCs) and somatic cell nuclear transfer-derived embryonic stem cells (nt-ESCs), genetically matched in vitro fertilization-derived ESCs (IVF-ESCs), and their respective differentiated cells (cardiomyocytes and endothelial cells). We generated the transcriptome and DNA methylome map in human pluripotent stem cells and their differentiated cells with single-nucleotide resolution. We compared the genetic (genetic makeup) and epigenetic (reprogramming approach) influence on the gene expression and DNA methylation profiles and found that genetic composition is the major contributor of the transcriptional and epigenetic variances observed in the undifferentiated and differentiated cells originated from different reprogramming mechanisms.
2017-12-06 | GSE94267 | GEO
Project description:We apply cellular reprogramming to an induced pluripotent cell state to human cell lines and primary samples exhibiting Chronic Myoloid Leukemia (CML). Addtionally, we generated an inducible CML BCR-ABL transgenic mouse model. Biological replicates (duplicates) were available for all samples. DNA methylation profiles for all cells were generated using Reduced Representation Bisulfite Sequencing (RRBS). DNA methylation profiling of human leukemia cell lines, primary cells, derived iPS cells as well as transgenic mouse models for CML in duplicates using RRBS.
2015-07-14 | E-GEOD-50456 | biostudies-arrayexpress
Project description:Despite rapid progress in characterizing transcription factor-driven reprogramming of somatic cells to an induced pluripotent stem (iPS) cell state, many mechanistic questions still remain. To gain insight into the earliest events in the reprogramming process, we systematically analyzed the transcriptional and epigenetic changes that occur during early factor induction after discrete numbers of divisions. We observed rapid, genome-wide changes in the euchromatic histone modification, H3K4me2, at more than a thousand loci including large subsets of pluripotency or developmentally related gene promoters and enhancers. In contrast, patterns of the repressive H3K27me3 modification remained largely unchanged except for focused depletion specifically at positions where H3K4 methylation is gained. These chromatin regulatory events precede transcriptional changes within the corresponding loci. Our data provide evidence for an early, organized, and population-wide epigenetic response to ectopic reprogramming factors that clarify the temporal order through which somatic identity is reset during reprogramming. Genome-scale DNA methylation was measured by reduced representation bisulfite sequencing (RRBS) during the initial phase in the reprogramming of mouse embryonic fibroblasts.
2011-01-03 | E-GEOD-26098 | biostudies-arrayexpress
Project description:Somatic cells can be reprogrammed to pluripotency using different methods. In comparison to pluripotent cells obtained through somatic nuclear transfer, induced pluripotent stem cells (iPSCs) exhibit a higher number of epigenetic errors. Furthermore, most of these abnormalities have been described to be intrinsic to the iPSC technology. Here we investigate whether the aberrant epigenetic patterns detected in iPSCs are specific to transcription factor-mediated reprogramming. We used germline stem cells (GSCs), which are the only adult cell type that can be converted into pluripotent cells (gPSCs) under specific culture conditions, and compared GSC-derived iPSCs and gPSCs at the transcriptomic, epigenetic and functional level. Our results show that both reprogramming methods generate indistinguishable states of pluripotency. GSC-derived iPSCs and gPSCs retained similar levels of donor cell-type memory and exhibited comparable numbers of reprogramming errors. Therefore, our study demonstrates that the epigenetic memory detected in iPSCs is not intrinsic to transcription-factor mediated reprogramming. Total RNA from 12 different in vitro mouse cell lines, 2 technical replicates per sample: germline stem cells (GSCs, 2 independent cell lines), GSC-derived induced pluripotent stem cells (iPSCs, 4 independent cell lines), germline-derived pluripotent stem cells (gPSCs, 4 independent cell lines), embryonic stem cells (ESCs), fibroblast-derived induced pluripotent stem cells (Fib-iPSCs)
2015-03-07 | E-GEOD-66613 | biostudies-arrayexpress
Project description:he ability to induce pluripotent stem cells from committed, somatic human cells provides tremendous potential for regenerative medicine. However, there is a defined neoplastic potential inherent to such reprogramming that must be understood and may provide a model for understanding key events in tumorigenesis. Using genome-wide assays, we identify cancer-related epigenetic abnormalities that arise early during reprogramming and persist in induced pluripotent stem cell (iPS) clones. These include hundreds of abnormal gene silencing events, patterns of aberrant responses to epigenetic-modifying drugs resembling those for cancer cells, and presence in iPS and partially reprogrammed cells of cancer-specific gene promoter DNA methylation alterations. Our findings suggest that by studying the process of induced reprogramming, we may gain significant insight into the origins of epigenetic gene silencing associated with human tumorigenesis, and add to means of assessing iPS for safety. Methylation was analyzed using Illumina's 27k Infinium platform for direct detection of methylation after bisulfite conversion. The overall methylation status was determined for several iPS lines and the pool cells from which they are derived. These methylation levels can be compared directly to those of cultured stem cells, differentiated cells and cancer cell lines.
2011-06-16 | E-GEOD-29872 | biostudies-arrayexpress
Project description:We report a method for specific capture of an arbitrary subset of genomic targets for single molecule bisulfite sequencing, and for digital quantitation of DNA methylation at a single nucleotide resolution. We used targeted bisulfite sequencing to characterize the changes of DNA methylation during the de-differentiation of human fibroblasts into hybrid stem cells, and into induced pluripotent stem cells. We compared the methylation level of approximately 66,000 CpG sites within 2020 CpG islands on chromosome 12, chromosome 20, and 34 selected regions. A total of 288 differentially methylated regions were identified between fibroblasts and pluripotent cells. Methylation cluster analysis revealed distinct methylation patterns between fibroblasts and pluripotent cells. Furthermore iPS cells are globally more methylated than human embryonic stem cells, which could be due to the reprogramming process. This targeted bisulfite sequencing method is particularly useful for efficient and large-scale analysis of DNA methylation in organisms with large genomes. Experiment Overall Design: Comparison of DNA methylation on 2020 CpG islands and 34 other selected regions among eleven human ES, iPS and fibroblast lines.
2009-08-28 | E-GEOD-15007 | biostudies-arrayexpress
Project description:We apply cellular reprogramming to an induced pluripotent cell state to human cell lines and primary samples exhibiting Chronic Myoloid Leukemia (CML). Addtionally, we generated an inducible CML BCR-ABL transgenic mouse model. Biological replicates (duplicates) were available for all samples. DNA methylation profiles for all cells were generated using Reduced Representation Bisulfite Sequencing (RRBS).
2015-07-14 | GSE50456 | GEO
Project description:Using the paradigm of in vitro differentiation of hESCs/iPSCs into retinal pigment epithelial (RPE) cells, we have recently profiled mRNA and miRNA transcriptomes to define a set of RPE mRNA and miRNA signature genes implicated in directed RPE differentiation. In this study, in order to understand the role of DNA methylation in RPE differentiation, we profiled genome-scale DNA methylation patterns using the method of reduced representation bisulfite sequencing (RRBS). We found dynamic waves of de novo methylation and demethylation in four stages of RPE differentiation. Integrated analysis of DNA methylation and RPE transcriptomes revealed a reverse-correlation between levels of DNA methylation and expression of a subset of miRNA and mRNA genes that are important for RPE differentiation and function. Gene Ontology (GO) analysis suggested that genes undergoing dynamic methylation changes were related to RPE differentiation and maturation. We further compared methylation patterns among human ESC- and iPSC-derived RPE as well as primary fetal RPE (fRPE) cells, and discovered that specific DNA methylation pattern is useful to classify each of the three types of RPE cells. Our results demonstrate that DNA methylation may serve as biomarkers to characterize the cell differentiation process during the conversion of human pluripotent stem cells into functional RPE cells. Study of DNA methylation patterns during RPE differentiation of pluripotent stem cells.
2014-05-28 | E-GEOD-43473 | biostudies-arrayexpress