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Mouse embryonic stem cells can differentiate via multiple paths to the same state

ABSTRACT: Mouse embryonic stem cells can differentiate via multiple paths to the same state

PROVIDER: PRJNA381612 | 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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Mouse embryonic stem cells can differentiate via multiple paths to the same state [array]

Project description:In embryonic development, cells must differentiate through stereotypical sequences of intermediate states to generate mature states of a particular fate. By contrast, direct programming can generate similar fates through alternative routes, by directly expressing terminal transcription factors. Yet the cell state transitions defining these new routes are unclear. We applied single-cell RNA sequencing to compare two mouse motor neuron differentiation protocols: a standard protocol approximating the embryonic lineage, and a direct programming method. Both undergo similar early neural commitment. Then, rather than transitioning through spinal intermediates like the standard protocol, the direct programming path diverges into a novel transitional state. This state has specific and abnormal gene expression. It opens a 'loop' or 'worm hole' in gene expression that converges separately onto the final motor neuron state of the standard path. Despite their different developmental histories, motor neurons from both protocols structurally, functionally, and transcriptionally resemble motor neurons from embryos.

2017-10-17 | GSE97360 | GEO

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

2017-10-17 | GSE97390 | GEO

Mouse embryonic stem cells can differentiate via multiple paths to the same state.

Project description:In embryonic development, cells differentiate through stereotypical sequences of intermediate states to generate particular mature fates. By contrast, driving differentiation by ectopically expressing terminal transcription factors (direct programming) can generate similar fates by alternative routes. How differentiation in direct programming relates to embryonic differentiation is unclear. We applied single-cell RNA sequencing to compare two motor neuron differentiation protocols: a standard protocol approximating the embryonic lineage, and a direct programming method. Both initially undergo similar early neural commitment. Later, the direct programming path diverges into a novel transitional state rather than following the expected embryonic spinal intermediates. The novel state in direct programming has specific and uncharacteristic gene expression. It forms a loop in gene expression space that converges separately onto the same final motor neuron state as the standard path. Despite their different developmental histories, motor neurons from both protocols structurally, functionally, and transcriptionally resemble motor neurons isolated from embryos.

| S-EPMC5648529 | biostudies-literature

Mouse embryonic stem cells can differentiate via multiple paths to the same state

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-10-17 | GSE97391 | GEO

Systematic drug perturbations of cancer cells reveal diverse exit paths from the proliferative state

Project description:Analysis of the time courses of gene expression profiles of breast cancer cell line MCF7 treated by 16 differentiation-inducing drugs at day 1, day 3 and day 5. The drugs are the screening results from the the JHCCL library (1,500 drugs). The hypothesis tested in the present study was that cancer cells exit the proliferative state via multiple paths. Results showed that cell state transition trajectories firstly diverged and later converged to a quiescient differentiated state MCF7 cells were cultured in 150mm dishes and treated 1/5/10 Î¼M of each of the 16 drugs (see details in Table S1-2). 14 plates of cells were left untreated as control samples. Cells were collected after 1, 3 and 5 days of drug treatment in RNeasy (Qiagen) lysis buffer and RNA was isolated according to the manufactureâs protocol and sent to Vancouver Prostate Center for transcript profiling.

2015-10-23 | E-GEOD-74281 | biostudies-arrayexpress

Mus musculus

Project description:Mouse embryonic stem cells can differentiate via multiple paths to the same state [array]

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Systematic drug perturbations of cancer cells reveal diverse exit paths from the proliferative state

2015-10-23 | GSE74281 | GEO

Mus musculus

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

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Monocytes differentiate into macrophages or dendritic cells along two alternative paths controlled by distinct regulatory networks

Project description:Monocytes differentiate into macrophages or dendritic cells along two alternative paths controlled by distinct regulatory networks

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Monocytes differentiate into macrophages or dendritic cells along two alternative paths controlled by distinct regulatory networks

Project description:During inflammation, monocytes differentiate within tissues into macrophages (mo-Mac) or dendritic cells (mo-DC). Whether these two progenies derive from alternative differentiation pathways or represent different stages along a continuum remains unclear. Here we addressed this question using temporal single-cell RNA sequencing in an in vitro model allowing the simultaneous differentiation of human mo-Mac and mo-DC. We evidenced divergent differentiation paths, with a fate decision occurring within the first 24 hours. We confirmed this result in vivo using a mouse model of peritonitis. Using a computational approach, we identified candidate transcription factors potentially involved in monocyte fate commitment. We demonstrated that IRF1 is necessary for mo-Mac differentiation, independently of its transcriptional control of interferon-stimulated genes. In addition, we validated the transcription factors ZNF366 and MAFF as regulators of mo-DC development. Our results indicate that mo-Mac and mo-DC represent two alternative cell fates requiring distinct transcription factors for their differentiation.

2023-03-27 | GSE218483 | GEO

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