RNA-seq of chemically reset human naive pluripotent stem cells
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ABSTRACT:
PROVIDER: PRJEB20388 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
Project description:Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here, we apply multi-omics to comprehensively define the chromatin-associated proteome, histone post-translational modifications and transcriptome of human naive and primed pluripotent stem cells. Integrating the chromatin-bound proteome and histone modification data sets reveals differences in the relative abundance and activities of distinct chromatin modules, identifying a strong enrichment of Polycomb Repressive Complex 2 (PRC2)-associated H3K27me3 in naive pluripotent stem cell chromatin. Single-cell approaches and human blastoid models reveal that PRC2 activity acts as a chromatin barrier restricting the differentiation of naive cells towards the trophoblast lineage, and inhibiting PRC2 promotes trophoblast fate induction and cavity formation. Our results establish that human naive pluripotent stem cells are not epigenetically unrestricted, but instead possess chromatin mechanisms that oppose the induction of alternative cell fates.
2022-05-06 | PXD028111 | Pride
Project description:In human embryos, naive pluripotent cells of the inner cell mass (ICM) generate epiblast, primitive endoderm and trophectoderm (TE) lineage, whence trophoblast cells derive. In vitro, naive pluripotent stem cells (PSCs) retain this potential and efficiently generate trophoblast stem cells (TSCs), while conventional PSCs form TSCs at low efficiency. Transient histone deacetylase and MEK inhibitions with LIF stimulation is used to chemically reset conventional to naive PSCs. Here we report that chemical resetting induces expression of both naive and TSC markers and of placental imprinted genes. A modified chemical resetting protocol allows for the fast and efficient conversion of conventional PSCs into TSCs, entailing shutdown of pluripotency genes and full activation of the trophoblast master regulators, without induction of amnion markers. Chemical resetting generates a plastic intermediate state, characterised by co-expression of naive and TSC markers, after which cells steer towards one of the two fates in response to the signalling environment. The efficiency and rapidity of our system will be useful to study cell fate transitions, and to generate models of placental disorders.
2023-01-30 | GSE184562 | GEO
Project description:This project aims at identifying missing proteins in naive pluripotent and trophoblastic stem cells in the framework of the human proteome project (HPP). To date, as much as 1343 missing proteins remain to be credibly identified essentially, but not entirely, by mass spectrometry. The present results also constitute a first step towards the identification of potential biological markers for assessing stem cells and early embryo development.
2023-03-11 | PXD035768 | Pride
Project description:These are 3 TMT10 samples. The indicated "standard" sub-samples all refer to the same biological sample (obtained as a mixture of all other samples), split and tagged as indicated, to play as a reference for normalization.
TMT10 sample1 contains the following sub-samples:
-TAG 126: Standard.
-TAG 127N: Day 3 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 127C: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 128N: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a VTN coating in RSeT medium.
-TAG 128C: Not relevant.
-TAG 129N: Not relevant.
-TAG 129C: Not relevant.
-TAG 130N: Not relevant.
-TAG 130C: RSet medium.
-TAG 131: Standard.
TMT10 sample2 contains the following sub-samples:
-TAG 126: Standard
-TAG 127N: Day 3 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 127C: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 128N: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a VTN coating in RSeT medium.
-TAG 128C: Not relevant.
-TAG 129N: Day 2 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 129C: Day 2 conditioned medium of naive human pluripotent stem cells cultured on a VTN coating in RSeT medium.
-TAG 130N: Not relevant.
-TAG 130C: RSet medium.
-TAG 131: Standard.
TMT10 sample3 contains the following sub-samples:
-TAG 126: Standard.
-TAG 127N: Day 3 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 127C: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 128N: Day 2 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 128C: Day 2 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 129N: Day 2 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 129C: Day 2 conditioned medium of naive human pluripotent stem cells cultured on a VTN coating in RSeT medium.
-TAG 130N: Not relevant.
-TAG 130C: RSet medium.
-TAG 131: Standard.
Detailed culture and processing methods are described in Cesare et al, under submission.
| MSV000086068 | MassIVE
Project description:Naive and primed human pluripotent stem cells (hPSC) provide valuable models to study cellular and molecular developmental processes. The lack of detailed information about cell-surface protein expression in these two pluripotent cell types prevents an understanding of how the cells communicate and interact with their microenvironments. Here, we used plasma membrane profiling to directly measure cell-surface protein expression in naive and primed hPSC. This unbiased approach quantified over 1700 plasma membrane proteins including those involved in cell adhesion, signalling and cell interactions. Notably, multiple cytokine receptors upstream of JAK-STAT signalling were more abundant in naive hPSC. In addition, functional experiments showed that FOLR1 and SUSD2 proteins are highly expressed at the cell surface in naive hPSC but are not required to establish human naive pluripotency. This study provides a comprehensive stem cell proteomic resource that uncovers differences in signalling pathway activity and has identified new markers to define human pluripotent states.
2020-04-17 | PXD015359 | Pride
Project description:This is a TMT6 sample containing the following sub-samples:
TAG 126: standard, used for normalization purposes, It is a mixture of different biological samples.
TAG 127: Lysate of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
TAG 128: Lysate of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium (mixed human and mouse cell population).
TAG 129: Lysate of naive human pluripotent stem cells cultured on VTN coating in RSeT medium.
TAG 130: Not relevant.
TAG 131: standard, used for normalization purposes, It is a mixture of different biological samples. Same as sub-sample with tag 126.
Detailed culture and processing methods are described in Cesare et al, under submission.
| MSV000086069 | MassIVE
Project description:Significant interest has been devoted to the isolation of human pluripotent stem cells displaying the naive state of mouse embryonic stem cells. However, to what extent naive human cells isolated in culture resemble pluripotent cells in vivo remains unclear. Here we present three lines of evidence indicating that naive pluripotent stem cells generated in the absence of transgenes share defining molecular signatures with the human pre-implantation embryo. First, a comprehensive analysis of the transposcriptome reveals that naive human cells have a retroelement expression profile of human cleavage stage embryos. Second, base-resolution mapping of the DNA methylome in naive human cells reveals a genome-wide reduction in CpG and non-CpG methylation levels. Third, female naive cells exhibit an X chromosome status that is similar to that of the human blastocyst. Our work demonstrates that pluripotent stem cells with epigenomic hallmarks of the early human embryo can be directly captured in vitro. Examine the methylomes of 6 naïve, 2 primed and 2 re-primed human embryonic stem cells
2016-07-18 | E-GEOD-75868 | biostudies-arrayexpress
Project description:Human pluripotent stem cells have two major pluripotent states, primed and naive, and the heterogeneity among cell lines in each pluripotent state remains a major unresolved problem. We showed that the overexpression of H1FOO-DD, which has a short expression period by fusing the destabilized domain to the maternal-specific linker histone H1FOO, together with OCT4, SOX2, KLF4 and LMYC in human somatic cells improves the quality of reprogramming to primed and naive pluripotency.
2024-05-01 | GSE253926 | GEO
Project description:We introduce a method for generating transgene-free and high-quality naive human induced pluripotent stem cells (iPSCs) using a modified Sendai virus (SeV) vector reprogramming system. This reprogramming method realizes the derivation of naive iPSCs from various somatic cells accompanied with fast and robust SeV vector removal at early passages. The established naive iPSCs have superior differentiation ability compared with iPSCs derived from conventional methods.
2022-12-15 | GSE207525 | GEO