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Mus musculus

ABSTRACT: Mouse embryonic stem cells can differentiate via multiple paths to the same state [RNA-seq]

PROVIDER: PRJNA381617 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5413310_1.fastq.gz	Fastqsanger.gz
	SRR5413310_2.fastq.gz	Fastqsanger.gz
	SRR5413311.fastq.gz	Fastqsanger.gz
	SRR5413311_1.fastq.gz	Fastqsanger.gz
	SRR5413311_2.fastq.gz	Fastqsanger.gz

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Project description:Current human pluripotent stem cells lack the transcription factor circuitry that governs the ground state of mouse embryonic stem cells (ESC). Here we report that short-term expression of two components, NANOG and KLF2, is sufficient to ignite other elements of the network and reset the human pluripotent state. Inhibition of ERK and protein kinase C signalling sustains a transgene-independent rewired state. Reset cells self-renew continuously without ERK signalling, are phenotypically stable and karyotypically intact. They differentiate in vitro and form teratomas in vivo. Metabolism is reprogrammed in reset cells with activation of mitochondrial respiration as in ESC. DNA methylation is dramatically reduced and transcriptome state is globally realigned across multiple cell lines. Depletion of ground state transcription factors, TFCP2L1 or KLF4 has marginal impact on conventional human pluripotent stem cells, but collapses the reset state. These findings demonstrate feasibility of installing and propagating functional control circuitry for ground state pluripotency in human cells. DNA methylation analysis in Conventional and Reset human embryonic stem cells by whole genome bisulfite sequencing, in triplicate, using the Illumina platform

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Project description:Comparison of transcriptional profiles between naive, primed and ground state pluripotency in mouse embryonic stem cells of the same genetic background

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Identification of novel embryonic differentiation stage by combined cell tracking and high dimensional protein imaging

Project description:Pluripotent mouse embryonic stem cells (ESCs) can differentiate to all germ layers and serve as an in vitro model of embryonic development. To better understand the differentiation paths traversed by ESCs committing to different lineages, we tracked individual differentiating ESCs by timelapse imaging followed by multiplexed high-dimensional Imaging Mass Cytometry (IMC) protein quantification. This links continuous live single-cell molecular NANOG and cellular dynamics quantification over 5-6 generations to protein expression of 37 different molecular regulators in the same single cells at the observation endpoints. Using this unique data set including kinship history and live lineage marker detection, we show that NANOG downregulation occurs generations prior to, but is not sufficient for neuroectoderm lineage commitment. Unexpectedly, we could identify a novel developmental cell type co-expressing both the canonical Sox1 neuroectoderm and FoxA2 endoderm markers in vitro and confirm the presence of such a population in the post-implantation embryo as well. RNASeq revealed cells co-expressing SOX1 and FOXA2 to have a unique cells state characterised by expression of both endoderm as well as neuroectoderm genes with lineage potential towards both germ layers.

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