Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA359212 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5134053_1.fastq.gz | Fastqsanger.gz | |||
| SRR5134053_2.fastq.gz | Fastqsanger.gz | |||
| SRR5134054_1.fastq.gz | Fastqsanger.gz | |||
| SRR5134054_2.fastq.gz | Fastqsanger.gz | |||
| SRR5134055_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
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 [RRBS]
| PRJNA359213 | ENA
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:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis
2018-08-02 | MSV000082680 | GNPS
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: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:Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the "gold standard" of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies. Duplicate cDNA libraries of two IVF-ESCs, three sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, and the parental fibroblast line were sequenced using Illumina HiSeq 2000. The sequence reads were mapped to hg19 reference genome and hits that passed quality filters were analyzed for differential expression.
2014-07-08 | E-GEOD-53094 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE29870: Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells (expression data) GSE29872: Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells (methylation data) Refer to individual Series
2011-06-16 | E-GEOD-29873 | biostudies-arrayexpress
Project description:Pluripotent stem cells can be obtained from spermatogonial stem cells (SSCs) through spontaneous reprogramming without transgenic introduction, but this process is inefficient and lacks mechanism exploration. Here, we reconstructed the progression trajectory of mouse SSC reprogramming by single-cell RNA sequencing and identified a bona fide pluripotent route as the successful reprogramming branch. Notably, we developed five-chemicals combination which could boost the reprogramming efficiency nearly 1000 times than previous study. More importantly, chemical induced germline-derived pluripotent stem cells (5C-gPSCs) with embryonic stem cell-like imprinting status were characterized as fully pluripotent via tetraploid complementation assay. Mechanistically, not only the expression of canonical markers, but also the global DNA demethylation and re-methylation features from epiblast to primordial germ cells and subsequent spermatogonia were remarkably observed during SSC reprogramming; meanwhile, biallelic methylation of most imprinting control regions (ICRs) in SSCs had been switched to monoallelic methylation in gPSCs through such stepwise reprogramming process. Compared to the extremely hypomethylated ICRs in developmental deficient chemical induced pluripotent stem cells (CiPSCs), we demonstrated the highly correlation between proper methylation of ICRs and fully pluripotency. Therefore, our work sheds light on the unique genetic- and epigenetic regulatory network of SSC reprogramming, providing novel insights to understand generic mechanisms for cell fate determination and the epigenetic related developmental disorders in regenerative medicine.
2023-02-07 | GSE186260 | GEO