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A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo [scRNA-seq]

ABSTRACT: We report the application of single-cell sequencing technology for high-throughput transcriptional profiling of differentiating mouse embryoid bodies. We make comparisons of the these transcriptional profiles to the transcriptional profiles of progenitors of a developing embryo.

ORGANISM(S): Mus musculus

PROVIDER: GSE114218 | GEO | 2018/08/15

REPOSITORIES: GEO

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A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo [bulk RNA-seq]

Project description:We report the application of bulk high-throughput transcriptional profiling of differentiating mouse embryoid bodies.

2018-08-15 | GSE114219 | GEO

Early embryoid body differentiation

Project description:Embryonic stem (ES) cells, when grown in suspension culture without feeders, spontaneously form round structures known as embryoid bodies. Given the appropriate conditions, these cells can differentiate over time into precursors of all three germ layers. Embryoid bodies, in a disorganized way, mimic early embryonic development to a certain extent and can be used as a synchronously differentiating large scale source of tissue for the study of biological determinants of early differentiation. Embryoid bodies have been used as a source for most early protocols that derive specific differentiated cell types from undifferentiated ES cells, although some protocols, notably those that derive neurons from ES cells, have moved on from EBs as a result of varying replicability and yield. We have decided to look at the transcriptomic profiles of embryoid bodies during the initial stages of embryoid body formation and differentiation, in order to pinpoint novel determinants of key developmental stages. Keywords: time course

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A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo.

Project description:Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent to differentiation. Here, we used a combination of bulk RNA-Seq, single cell RNA-Seq, and bioinformatics analyses to dissect the cell types that emerge during directed differentiation of mouse embryonic stem cells as embryoid bodies and we compared them to spatially and temporally resolved transcriptional profiles of early embryos. Our single cell analyses of the day 4 embryoid bodies revealed three populations which had retained related yet distinct pluripotent signatures that resemble the pre- or post-implantation epiblast, one population of presumptive neuroectoderm, one population of mesendoderm, and four populations of neural progenitors. By day 6, the neural progenitors predominated the embryoid bodies, but both a small population of pluripotent-like cells and an anterior mesoderm-like Brachyury-expressing population were present. By comparing the day 4 and day 6 populations, we identified candidate differentiation paths, transcription factors, and signaling pathways that mark the in vitro correlate of the transition from the mid-to-late primitive streak stage.

| S-EPMC6579609 | biostudies-literature

A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo

Project description:A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo

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A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo [scRNA-seq]

Project description:A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo [scRNA-seq]

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A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo [bulk RNA-seq]

Project description:A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo [bulk RNA-seq]

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A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo

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

2018-08-15 | GSE114220 | GEO

Relocalization of retinoic acid receptors from non-canonical to canonical spaced binding elements during embryoid body differentiation

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scRNAseq of embryoid bodies derived from control mESC or mESC pulsed with DUX expression

Project description:scRNAseq identifies extra-embryonic cell type preference for DUX-pulsed mESC differentiating into embryoid bodies.

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