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T cell regeneration from pluripotent stem cells by defined transcription factors [T cell receptors (TCR)]

ABSTRACT: We established a de novo approach of generating T cells from mouse ESC/iPSC.

ORGANISM(S): Mus musculus

PROVIDER: GSE121374 | GEO | 2020/07/31

REPOSITORIES: GEO

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T cell regeneration from pluripotent stem cells by defined transcription factors [T cells [CD4 and CD8])

Project description:We established a de novo approach of generating T cells from mouse ESC/iPSC by defined transcription factors.

2020-07-31 | GSE121373 | GEO

Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors [RNA-Seq]

Project description:Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. Both cell types shared similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs have comparable numbers of de novo coding mutations but significantly higher than parthenogenetic ESCs. Similar to iPSCs NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes, similarly to iPSCs. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of the underlying technique. RNA sequencing analysis was performed on a total of 12 human cell lines, including: an isogenic set of 3 nuclear-transfer embryonic stem cell (NT-ESC) lines, 2 RNA-reprogrammed induced pluripotent stem cell (iPSC) lines and their parental neonatal fibroblast cell line; an isogenic set of 1 NT-ESC line, 3 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 1 control embryonic stem cell (ESC) line.

2014-11-06 | E-GEOD-61656 | biostudies-arrayexpress

T cell regeneration from pluripotent stem cells by defined transcription factors [T cell receptors (TCR)]

Project description:T cell regeneration from pluripotent stem cells by defined transcription factors [T cell receptors (TCR)]

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Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors [DNA methylation profiling]

Project description:Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. Both cell types shared similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs have comparable numbers of de novo coding mutations but significantly higher than parthenogenetic ESCs. Similar to iPSCs NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes, similarly to iPSCs. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of the underlying technique. Genome-wide DNA methylation profiling by Illumina Infinium HumanMethylation 450K Beadchip was performed on a total of 21 human cell lines, including: an isogenic set of 3 nuclear-transfer embryonic stem cell (NT-ESC) lines, 2 RNA-reprogrammed induced pluripotent stem cell (iPSC) lines and their parental neonatal fibroblast cell line; an isogenic set of 1 NT-ESC line, 6 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 7 control embryonic stem cell (ESC) lines.

2014-11-06 | E-GEOD-61461 | biostudies-arrayexpress

CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming

Project description:Analysis of different iPSC clones in comparison to parental fibroblasts and Pluripotent ESC and iPSC lines Total RNA obtained from iPSC clones generated with CytoTune reprogramming of BJ Fbiroblasts and compared to parent BJ fibroblasts and known pluripotent H9 ESC and Gibco Episomal iPSC lines.

2013-11-05 | E-GEOD-51980 | biostudies-arrayexpress

Myeloid, B, and T lineage regeneration from pluripotent stem cells by defined transcription factors

Project description:Generating prolonged multi-lineage hematopoiesis from pluripotent stem cells (PSCs), an unlimited cell source, is a crucial aim for regenerative hematology. In this study, we used a gene-edited PSC line and revealed that simultaneous expression of three transcription factors, Runx1, Hoxa9, and Hoxa10, drove robust emergence of induced hematopoietic progenitor cells (iHPCs). The iHPCs engrafted successfully in wild type animals and repopulated abundant and complete myeloid, B, and T lineage mature cells in primary and secondary C57BL/6 recipients. The regenerative multi-lineage hematopoiesis distributed normally in multiple organs, persisted over six months, and eventually declined over time with no leukemogenesis. Transcriptome characterization of regenerative myeloid, B, and T cells at the single cell resolution further projected their identities to natural cell counterparts. Thus, we provide strong genetic evidence that co-expression of exogenous Runx1, Hoxa9, and Hoxa10 simultaneously leads to long-term reconstitution of myeloid, B, and T lineages using PSC-derived iHPCs as cell source.

2023-02-14 | GSE217945 | GEO

T cell regeneration from pluripotent stem cells by defined transcription factors

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-07-31 | GSE121375 | GEO

CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming

Project description:Analysis of different iPSC clones in comparison to parental fibroblasts and Pluripotent ESC and iPSC lines

2013-11-05 | GSE51980 | GEO

SUMO safeguards somatic and pluripotent cell identities by enforcing distinct chromatin states

Project description:Purposes: (1) compare the SUMO chromatin landscape between mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESc) (2) Decipher how hyposumoylation enhances MEF to induced pluripotent stem cells (iPSc) reprogramming (3) Decipher how hyposumoylation enhances ESc to 2C-like cells conversion. Methods : (1) ChIP-seq in MEFs and ESc for SUMO isoforms and histone marks. (2) ChIP-seq for transcription factors and histone marks at day 4 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). ATAC-Seq at day 4 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). RNA-Seq in MEFs, iPSc, at day 4 and day 7 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). (3) RNA-Seq in ESc comparing wild-type (siCtrl) and hyposumoylated cells (siUbc9). Results: (1) SUMO chromatin landscape is highly different between MEFs and ESc and associates to distinct chromatin marks. (2) Hyposumoylation enhances MEFs to iPSc reprogramming by favoring the extinction of the MEF transcriptional program and redistributing pluripotency factors from MEF enhancers toward ES enhancers. (3) Hyposumoylation enhances ES to 2C-like conversion by destabilizing heterochromatin thus resulting in an activation of the 2-cell transcriptional program. Conclusion: SUMO at chromatin is gate-keeper of cell-identity.

2018-10-24 | GSE99009 | GEO

The NIH Human Pluripotent Stem Cell Database (Agilent, mRNA)

Project description:To better understand the extent to which induced pluripotent stem cells (iPSCs) faithfully recapitulate the characteristics of embryonic stem cells (ESCs) under (undiff)erentiated condition, KSR condition and FBS condition and how both compare to somatic tissues under these conditions, we employed whole-genome transcriptome analysis on all twenty one hESC lines available on the pre-2008 NIH Human Pluripotent Stem Cell Registry, eight human iPSCs derived at NIH by retroviral transduction of human fibroblasts and twenty human somatic tissues. One standard culture protocol was used in conjunction with rigorous quality control. Expanded description of methods used and are available at: http://stemcelldb.nih.gov. 230 samples: 44 human ESC (UNDIFF), 16 human iPSC (UNDIFF) 44 human ESC (KSR), 15 human iPSC (KSR), 44 human ESC (FBS), 15 human iPSC (FBS), 1 human Brain, 1 human Placenta, 1 human Skeletal Muscle, 1 human Heart, 1 human Liver, 1 human Lung, 1 human Kidney, 1 human Esophagus, 1 human Ovary, 1 human Testes, 1 human Spleen, 1 human Adipose, 1 human Thyroid, 1 human Thymus, 1 human Small Intestine, 1 human Prostate, 1 human Cervix, 1 human Colon, 1 human Bladder, 1 human Trachea) and 32 processing controls (UniRef).

2012-10-31 | E-GEOD-32923 | biostudies-arrayexpress

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