Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.

The ground or naive pluripotent state of human pluripotent stem cells (hPSCs), which was initially established in mouse embryonic stem cells (mESCs), is an emerging and tentative concept. To verify this vital concept in hPSCs, we performed a multivariate meta-analysis of major hPSC datasets via the...

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Autores principales:	Kory R Johnson, Barbara S Mallon, Yang C Fann, Kevin G Chen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bbc2306d4c814b46a7088f9ea8db8f19
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spelling	oai:doaj.org-article:bbc2306d4c814b46a7088f9ea8db8f192021-12-02T20:04:05ZMultivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.1932-620310.1371/journal.pone.0251461https://doaj.org/article/bbc2306d4c814b46a7088f9ea8db8f192021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0251461https://doaj.org/toc/1932-6203The ground or naive pluripotent state of human pluripotent stem cells (hPSCs), which was initially established in mouse embryonic stem cells (mESCs), is an emerging and tentative concept. To verify this vital concept in hPSCs, we performed a multivariate meta-analysis of major hPSC datasets via the combined analytic powers of percentile normalization, principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and SC3 consensus clustering. This robust bioinformatics approach has significantly improved the predictive values of our meta-analysis. Accordingly, we revealed various similarities or dissimilarities between some naive-like hPSCs (NLPs) generated from different laboratories. Our analysis confirms some previous studies and provides new evidence concerning the existence of three distinct naive-like pluripotent states. Moreover, our study offers global transcriptomic markers that define diverse pluripotent states under various hPSC growth protocols.Kory R JohnsonBarbara S MallonYang C FannKevin G ChenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0251461 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kory R Johnson Barbara S Mallon Yang C Fann Kevin G Chen Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.
description	The ground or naive pluripotent state of human pluripotent stem cells (hPSCs), which was initially established in mouse embryonic stem cells (mESCs), is an emerging and tentative concept. To verify this vital concept in hPSCs, we performed a multivariate meta-analysis of major hPSC datasets via the combined analytic powers of percentile normalization, principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and SC3 consensus clustering. This robust bioinformatics approach has significantly improved the predictive values of our meta-analysis. Accordingly, we revealed various similarities or dissimilarities between some naive-like hPSCs (NLPs) generated from different laboratories. Our analysis confirms some previous studies and provides new evidence concerning the existence of three distinct naive-like pluripotent states. Moreover, our study offers global transcriptomic markers that define diverse pluripotent states under various hPSC growth protocols.
format	article
author	Kory R Johnson Barbara S Mallon Yang C Fann Kevin G Chen
author_facet	Kory R Johnson Barbara S Mallon Yang C Fann Kevin G Chen
author_sort	Kory R Johnson
title	Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.
title_short	Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.
title_full	Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.
title_fullStr	Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.
title_full_unstemmed	Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.
title_sort	multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/bbc2306d4c814b46a7088f9ea8db8f19
work_keys_str_mv	AT koryrjohnson multivariatemetaanalysisrevealsglobaltranscriptomicsignaturesunderlyingdistincthumannaivelikepluripotentstates AT barbarasmallon multivariatemetaanalysisrevealsglobaltranscriptomicsignaturesunderlyingdistincthumannaivelikepluripotentstates AT yangcfann multivariatemetaanalysisrevealsglobaltranscriptomicsignaturesunderlyingdistincthumannaivelikepluripotentstates AT kevingchen multivariatemetaanalysisrevealsglobaltranscriptomicsignaturesunderlyingdistincthumannaivelikepluripotentstates
_version_	1718375625872375808

Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states.

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