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Transcriptional profiling of human naive embryonic stem cells

ABSTRACT: Human pluripotent cell lines were derived from blastocyst-stage embryos and propagated in self-renewal conditions that maintain features of naive pluripotency characteristic of mouse embryonic stem cells. Transcriptional activity of HNES1, HNES2 and HNES3 cell lines was assessed with RNA-seq.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Paul Bertone

PROVIDER: E-MTAB-4461 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass.

Guo Ge G von Meyenn Ferdinand F Santos Fatima F Chen Yaoyao Y Reik Wolf W Bertone Paul P Smith Austin A Nichols Jennifer J

Stem cell reports 20160303 4

Conventional generation of stem cells from human blastocysts produces a developmentally advanced, or primed, stage of pluripotency. In vitro resetting to a more naive phenotype has been reported. However, whether the reset culture conditions of selective kinase inhibition can enable capture of naive epiblast cells directly from the embryo has not been determined. Here, we show that in these specific conditions individual inner cell mass cells grow into colonies that may then be expanded over mul ...[more]

PMID: 26947977

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Karyotype analysis of human naive embryonic stem cells

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2016-03-01 | E-MTAB-4463 | biostudies-arrayexpress

DNA methylation profiling of human naive embryonic stem cells

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Domains of genomewide gene expression dysregulation in Down syndrome

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Single cell Hi-C reveals cell-to-cell variability in chromosome structure

Project description:Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation, affecting most domains in most nuclei. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns. Mouse Th1 single-cell Hi-C maps were produced and paired-end sequenced. 10 single-cell samples and a multi-sample pool together with a population Hi-C sample are included.

2013-09-26 | E-GEOD-48262 | biostudies-arrayexpress

PAR-CLIP-seq reveals RNAs directly interacting with CTCF in human transformed cell line U2OS

Project description:This experiment sought to determine the genome-wide interactome of CTCF in human cells. PAR-CLIP seq for CTCF was performed in U2OS cells in 2 biological replicates

2014-03-18 | E-GEOD-53554 | biostudies-arrayexpress

PAR-CLIP for JARID2 in mouse embryonic stem cells

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2015-09-10 | E-GEOD-72860 | biostudies-arrayexpress

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