Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA118849 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome wide comparison of gene expression between EpiSC lines derived from fertilized (FT) embryos and somatic cell nuclear transfer (NT) embryos. EpiSC lines were derived from fertilized and somatic cell nuclear transfer embryos and cultured until 15 to 20 passages. RNA was then extracted in order to compare transcriptomic profiles.
2010-02-05 | GSE17402 | GEO
Project description:Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we perform allele-specific RNA-Seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic stages and in pluripotent cell lines. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos or from embryos obtained after nuclear transfer (NT), as well as B6D2F1 ESCs and EpiSCs derived after parthenogenetic activation (PGA). Notably, the PGA-derived cell lines contain a mosaic genotype due to genomic recombination occurring in the parental B6D2F1 oocyte during meiosis. As the homozygous genomic regions of the PGA-derived cells are not compatible with allele-specific RNA-Seq, we developed an RNA-Seq based genotyping strategy that allows identification of the informative heterozygous regions. Global imprinting analysis shows that ESC lines largely lose imprints as compared to their corresponding embryonic tissues. Fertilized EpiSC and EpiSC-NT lines generally maintain imprinted gene expression. However, two EpiSC-NT lines show aberrant silencing of Rian and Meg3, two critically imprinted genes in mouse iPSCs. EpiSC-PGA lines display loss of imprinting, with known paternally-expressed genes being silenced and known maternally-expressed genes consistently showing doubled expression. Interestingly, most female EpiSC lines show monoallelic expression of Xist and full skewing of X inactivation, suggesting a (near) clonal origin. Together, our analysis provides a comprehensive overview of imprinted gene expression in pluripotency and provides a benchmark to allow identification of cell lines that faithfully maintain imprinted gene expression and therefore retain full developmental potential.
2019-02-16 | GSE101292 | GEO
Project description:Nuclear transfer (NT) has potential applications in agriculture and biomedicine, but the technology is hindered by low efficiency. Global gene expression analysis of clones is important for the comprehensive study of nuclear reprogramming. Here, we compared global gene expression profiles of individual bovine NT blastocysts with their somatic donor cells and fertilized control embryos utilizing cDNA microarray technology. The NT embryos’ gene expression profiles were drastically different from those of their donor cells and closely resembled those of the naturally fertilized embryos. Our findings demonstrate that the NT embryos have undergone significant nuclear reprogramming by the blastocyst stage; however, problems may occur during re-differentiation for tissue- and organogenesis, and small reprogramming errors may be magnified downstream in development. Keywords: cDNA microarray
2005-11-30 | GSE3568 | GEO
Project description:We have developed a nuclear transfer (NT) system in which somatic nuclei are transplanted into mouse embryos arrested at the 4-cell stage. The transplanted somatic nuclei show swelling and epigenetic reprogramming towards 4-cell-like nuclei. To assess genome-wide transcriptional reprogramming of the injected nuclei, the newly transcribed genes in NT embryos were examined by RNA-seq analyses. As a control, NT was also performed using mouse embryos at the 2-cell stage.
2021-11-03 | GSE162345 | GEO
Project description:Human pluripotent stem cells hold great potential for regenerative medicine, but existing cell types have imitations. Human embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the “gold standard”, but are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) can be produced from somatic cells by forced expression of pluripotency-associated factors, but are prone to genetic and epigenetic aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming, or secondary to the reprogramming method, we employed an alternative approach by somatic cell nuclear transfer (SCNT). SCNT-based reprogramming to NT-ESCs is mediated by factors present in oocyte’s cytoplasm, thus mimicking early embryogenesis. We generated genetically matched pluripotent stem cells and conducted genome-wide genetic, epigenetic and transcriptional analyses. We discovered that unlike iPSCs, NT-ESCs have a low burden of de novo copy number variations (CNVs), reflecting superior maintenance of genetic stability. Moreover, DNA methylation and transcriptome profiles of NT-ESCs corresponded closely to those of IVF-ESCs. In contrast, iPSCs harbored methylation abnormalities including residual CpG methylation typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT with the potential to satisfy the clinical requirements for cell replacement therapies. Bisulphite converted DNAs of two IVF-ESCs, two sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, and the parental fibroblast were hybridized to the Illumina Infinium HumanMethylation 450K Beadchip
2014-07-08 | E-GEOD-53060 | biostudies-arrayexpress
Project description:Enucleated oocytes have the remarkable ability to reprogram somatic nuclei back to totipotency. Here we investigate genome-scale DNA methylation patterns after nuclear transfer and identify specific targets for DNA demethylation as well as NT specific limitations. We find that the ooplasm can confer similar demethylation patterns in both processes except at some repetitive element classes and that germ-line associated promoters are specifically targeted in NT. Comparison of DNA methylation patterns in murine fertilization and somatic cell nuclear transfer
2012-08-10 | E-GEOD-38711 | biostudies-arrayexpress
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. 16 matched samples, two IVF-ESCs, five sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, the parental fibroblast line, and the sperm and oocyte donor were genotyped using the Illumina Omni5, which interrogates 4.3 million SNPs across the human genome. Additionally, matched samples from a patient with Leigh syndrome, a NT-ESC line, three iPSC lines, and the parental fibroblast line were genotyped using the Illumina Omni5.
2014-07-08 | E-GEOD-53141 | biostudies-arrayexpress
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: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:Nuclear reprogramming reinstates totipotency or pluripotency in somatic cells by changing their genetic transcription. This technology is widely used in medicine, animal husbandry and other industries. However, certain deficiencies, such as the poor developmental ability of reprogrammed nuclear transfer (NT) embryos and the low birth rate (less than 5%) of cloned animals, severely restrict the promotion of this technology. Multiple nuclear reprogramming barriers likely exist in the process of somatic nuclear reprogramming. Furthermore, the NT embryos obtained via this technology have transcriptional defects in embryonic development. To address these problems, in this study, two types of NT embryos were constructed using the same genetic background in mice. We detected the full transcriptome of all stages of NT embryos using single-cell RNA-seq and obtained the following results: 1) NT embryos have translation initiation defects during the minor zygotic genome activation (ZGA) period; NT embryos display RNA processing and RNA modification defects during the major ZGA period, and their protein kinase activity in protein phosphorylation exhibits defects during blastocyst formation; and 2) 2003 constant genes cannot be reprogrammed in cumulus cells (CCs) and mouse embryo fibroblast cells (MEFs); of these constant genes, 399/583 reprogramming barrier genes (RBGs) continue to mis-transcribe from the pronuclear stage to the blastula stage, and the same 136 RBGs are found in both the CCs and MEFs. The main functions of these RBGs is to positively regulate certain factors. In conclusion, our study offers full transcriptome blueprints of all stages of CC donor NT embryos, MEF donor NT embryos and in vivo embryos and reveals new transcriptional defects and reprogramming barriers in nuclear reprogramming. These findings provide insight for further mechanism studies investigating somatic nuclear reprogramming.
2018-08-11 | GSE113164 | GEO