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Gene expression in primed and chemically reset (cR) naïve human iPSCs, and naïve-converted cells after co-culture with mouse embryonic stem cells

ABSTRACT: Gene expression in primed and chemically reset (cR) naïve human iPSCs, and naïve-converted cells after co-culture with mouse embryonic stem cells

PROVIDER: PRJNA893005 | ENA |

REPOSITORIES: ENA

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Gene expression in primed and chemically reset (cR) naïve human iPSCs, and naïve-converted cells after co-culture with mouse embryonic stem cells

Project description:We compared the global transcriptome between mESC co-culture-mediated naïve-like hiPSCs and cR cells together with their parental primed cells.

2024-08-08 | GSE216338 | GEO

RNA-seq of chemically reset human naive pluripotent stem cells

Project description:A simple method is presented to reset human pluripotent cells to a naive state via transient histone deacetylase inhibition and maintenance in chemically-defined naive stem cell culture media. Cells can be reset without transgenes and expanded continuously either on feeders or alternative substrates in feeder-free conditions. Multiple cell lines of varying origin were reset and characterised in parallel with conventionally cultured counterparts.

2017-08-07 | E-MTAB-5674 | biostudies-arrayexpress

RNA-seq of chemically reset human naive pluripotent stem cells

Project description:RNA-seq of chemically reset human naive pluripotent stem cells

| PRJEB20388 | ENA

Reproduction of reset cell

Project description:Functional-assay limitations are an emerging issue in characterizing human pluripotent stem cells (hPSCs). With rodent PSCs, chimera formation, using pre-implantation embryos, is the gold-standard assay of pluripotency. In hPSCs, this can only be monitored via teratoma formation or in vitro differentiation, as ethical concerns preclude generation of human-animal chimera. To circumvent this issue, we established a functional assay utilizing interspecific blastocyst injection and in vitro culture (interspecies in vitro chimera assay). The assay uses mouse pre-implantation embryos and human PSCs to make interspecies chimeras cultured in vitro to the early egg cylinder stage. When hiPSCs, both conventional and naive type, which called M-bM-^@M-^\reset cellM-bM-^@M-^], were injected into mouse embryos and cultured. The cells were never integrated into the epiblast of egg cylinder stage-embryo. These results suggest that hPSCs, including naM-CM-/ve type, are unable to form chimera with mouse embryo. Reset cells were converted from conventional human iPSC line PB004, and then compared their gene expression profile with or without transgene overexpression induced by doxycyclin treatment.

2015-03-10 | E-GEOD-66657 | biostudies-arrayexpress

Reproduction of reset cell

Project description:Functional-assay limitations are an emerging issue in characterizing human pluripotent stem cells (hPSCs). With rodent PSCs, chimera formation, using pre-implantation embryos, is the gold-standard assay of pluripotency. In hPSCs, this can only be monitored via teratoma formation or in vitro differentiation, as ethical concerns preclude generation of human-animal chimera. To circumvent this issue, we established a functional assay utilizing interspecific blastocyst injection and in vitro culture (interspecies in vitro chimera assay). The assay uses mouse pre-implantation embryos and human PSCs to make interspecies chimeras cultured in vitro to the early egg cylinder stage. When hiPSCs, both conventional and naive type, which called “reset cell”, were injected into mouse embryos and cultured. The cells were never integrated into the epiblast of egg cylinder stage-embryo. These results suggest that hPSCs, including naïve type, are unable to form chimera with mouse embryo.

2015-03-10 | GSE66657 | GEO

REM-CR

Project description:REM-CR

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Candidatus Symbiobacter mobilis CR strain:CR

Project description:Candidatus Symbiobacter mobilis CR strain:CR Genome sequencing

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Fundulus heteroclitus exposed to Cr(III)

Project description:Cr(III) is the dominant toxicant at some Superfund sites within the United States and therefore we are interested in its effects. Cr(III)’s mechanisms are not well studied or understood because of its low bioavailability. We have attempted to characterize the effects of Cr(III) on gene expression in the liver of adult male Fundulus heteroclitus. The NOEC and LOEC were determined at 32 and 64mg/L, respectively, by measuring growth after exposing juveniles for 30 days. Secondary exposures were performed with adult males at 32mg/L, livers excised, and RNA extracted. Microarrays were probed with cDNA from untreated or Cr(III)-exposed adult fish and gene expression was quantified. Cr(III) at 32mg/L altered the expression of 5 genes, including GSTalpha, GSTtheta, and ALDH4. Ultimately, we anticipate using this gene expression information to determine whether chromium is available at potentially adverse concentrations in contaminated sites. Keywords: dose response

2005-07-15 | GSE2807 | GEO

Microarray expression profiling of conventional and reset human pluripotent stem cells

Project description:Human pluripotent cells were reset to ground state pluripotency by transient overexpression of NANOG and KLF2 and subsequent inhibition of ERK and protein kinase C. Transcriptional profiling of H9 parental and clonal lines, and induced pluripotent stem cells derived from adult fibroblast and adipose cell types was carried out in reset and conventional culture conditions.

2014-09-10 | E-MTAB-2856 | biostudies-arrayexpress

RNA sequencing of conventional and reset human pluripotent stem cells

Project description:Human pluripotent cells were reset to ground state pluripotency by transient overexpression of NANOG and KLF2 and subsequent inhibition of ERK and protein kinase C. Transcriptional profiling of reset cells and conventional pluripotent stem cell cultures was carried out by RNA-seq, in tandem with mouse embryonic stem cells propagated under similar conditions to assess the combinatorial effects of MEK inhibitor PD0325901, GSK3 inhibitor CHIR99021 and PKC inhibitor Go6983.

2014-09-10 | E-MTAB-2857 | biostudies-arrayexpress

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