ScRNA-seq for mEpiSCs (epiblast stem cells) differentiated to posterior primitive streak (PPS) in vitro, in a monolayer
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB55466 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR10092600.fastq.gz | Fastqsanger.gz | |||
| ERR10092700.fastq.gz | Fastqsanger.gz | |||
| ERR10092800.fastq.gz | Fastqsanger.gz | |||
| ERR10092900.fastq.gz | Fastqsanger.gz |
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Project description:EpiSCs established from murine epiblast were differentiated to posterior primitive streak (PPS) and analyzed using scRNA-seq to investigate identity and homogeneity of the resulting population.
2022-11-30 | E-MTAB-12106 | biostudies-arrayexpress
Project description:During mammalian embryonic development, the primitive streak is initiates the differentiation of pluripotent epiblast cells into germ layers. Pluripotency can be reacquired in committed somatic cells using a combination of handful transcription factors, such as OCT3/4, SOX2, KLF4 and c-MYC (hereafter referred to as OSKM), albeit with low efficiency . Here we show that, during the OSKM-induced reprogramming process toward pluripotency in human cells, intermediate cells transiently show gene expression profiles resembling mesendoderm, which is a major component of the primitive streak. Based on these findings, we discover that forkhead box H1 (FOXH1), a transcription factor required for anterior primitive streak specification during early development, significantly enhances the reprogramming efficiency of human fibroblasts by promoting their maturation, including the mesenchymal to epithelial transition and the activation of late pluripotent markers. These results demonstrate that during the reprogramming process, human somatic cells go through a transient state that resembles mesendoderm.
2014-04-24 | GSE50206 | GEO
Project description:In birds and mammals, all mesoderm cells are generated from the primitive streak. Nascent mesoderm cells contain unique dorso-ventral (D/V) identities depending on their relative ingression position along the streak. Molecular mechanisms controlling this initial phase of mesoderm diversification are not well-understood. Using chick model, we generated high-quality transcriptomic datasets of different streak regions and analyzed their molecular heterogeneity.
2010-07-29 | GSE22230 | GEO
Project description:During mammalian embryonic development, the primitive streak is initiates the differentiation of pluripotent epiblast cells into germ layers. Pluripotency can be reacquired in committed somatic cells using a combination of handful transcription factors, such as OCT3/4, SOX2, KLF4 and c-MYC (hereafter referred to as OSKM), albeit with low efficiency . Here we show that, during the OSKM-induced reprogramming process toward pluripotency in human cells, intermediate cells transiently show gene expression profiles resembling mesendoderm, which is a major component of the primitive streak. Based on these findings, we discover that forkhead box H1 (FOXH1), a transcription factor required for anterior primitive streak specification during early development, significantly enhances the reprogramming efficiency of human fibroblasts by promoting their maturation, including the mesenchymal to epithelial transition and the activation of late pluripotent markers. These results demonstrate that during the reprogramming process, human somatic cells go through a transient state that resembles mesendoderm. Human differentiated progeny derived from pluripotent stem cells, N=13 Human undifferentiated pluripotent stem cells, N=6 Transgenic ESC line, N=6 Human tissues, N=29 Human tissue-derived cells, N=20 Human nascent reprogrammed cells, N=95 Mouse cells, N=12
2014-04-24 | E-GEOD-50206 | biostudies-arrayexpress
Project description:Transcriptional profiling of the preingression epiblast versus lateral epiblast, of preingression epiblast from control embryos treated with the DMSO carrier vehicle (0.5%) versus embryos treated with SU5402, U0126 or LY294002. Embryos were stages 5-6 at time of tissue isolation. The preingression epiblast (E2 region) is the region of epiblast just lateral to the primitive streak. Lateral epiblast is the E3 region. Two condition experiment. Samples for each condition isolated from at least 30 embryos. The experiments used isolated preingression epiblast, which is defined as the region of epiblast adjacent to the primitive streak that will ingress through the primitive streak. Preingression epiblast was isolated by microdissection using tungsten needles from control embryos or embryos treated with SU5402, U0126 or LY294002.
2011-02-20 | E-GEOD-27403 | biostudies-arrayexpress
Project description:In birds and mammals, all mesoderm cells are generated from the primitive streak. Nascent mesoderm cells contain unique dorso-ventral (D/V) identities depending on their relative ingression position along the streak. Molecular mechanisms controlling this initial phase of mesoderm diversification are not well-understood. Using chick model, we generated high-quality transcriptomic datasets of different streak regions and analyzed their molecular heterogeneity. Streak tissues were dissected from stage-matched HH4 chick embryos and were further divided into four equal pieces along its anterio-posterior length (termed “A”, “B”, “C” and “D”, with “A” representing most anterior and therefore most dorsal and “D” most posterior and therefore most ventral). Each of the four regions was represented by three independent samples (n=3), with each sample containing 5-7 μg total RNA derived from 85-93 pooled pieces. 5 μg of RNA from each sample were used to screen Affymetrix Chicken Genome Array without an amplification step.
2010-07-29 | E-GEOD-22230 | biostudies-arrayexpress
Project description:EpiSCs (epiblast stem cells) are murine pluripotent stem cells derived from the epiblast of a post-implantation embryo. These cells are primed to differentiate towards embryonic germ layers and are a useful model to study these early developmental events. PGR (progesterone receptor) is a nuclear receptor described mainly in the context of fertility and breast cancer. We noticed that it is also a TF that is expressed in primed EpiSCs, but not in naive mESCs and is further upregulated during mesoderm specification. We hypothesized that it is involved in differentiation to primitive streak and mesoderm progenitors. To test this hypothesis we generated EpiSCs with a genetic knockout of PGR using CRISPR-Cas9-mediated knock-in of an antibiotic resistance cassette. Differentiation of the wild-type and knockout cells and comparison of the different cell types allowed us to conclude that PGR is important for acquiring extraembryonic mesoderm fate and modulates cardiac differentiation, specifically it ensures that correct pools of FHF (first heart field) and SHF (second heart field) are being produced. Our study sheds light on previously unappreciated role of PGR in early embryonic development.
2022-11-30 | E-MTAB-12104 | biostudies-arrayexpress
Project description:Specifying the primitive streak (PS) guides stem cell differentiation in vitro, however much remains to be learned about the transcription networks that direct anterior and posterior PS cells (APS and PPS, respectively) to differentiate to distinct mesendodermal subpopulations. Here, we show that APS genes are predominantly induced in YAP1-/- hESCs in response to ACTIVIN. This finding establishes the Hippo effector YAP1 as a master regulator of PS specification, functioning to repress ACTIVIN-regulated APS genes in hESCs. Moreover, transient exposure of wild-type hESCs to dasatinib, a potent C-SRC/YAP1 inhibitor, enables differentiation to APS-derived endoderm and cardiac mesoderm in response to ACTIVIN. Importantly, these cells can differentiate efficiently to normal beating cardiomyocytes without the cytoskeletal defect seen in YAP1-/- hESC-derived cardiomyocytes. Overall, we uncovered an induction mechanism to generate APS cells using a cocktail of ACTIVIN and YAP1i molecules that holds practical implications for hESC and iPSC differentiation into distinct mesendodermal lineages.
2018-11-14 | GSE121877 | GEO
Project description:During gastrulation, epiblast cells are pluripotent and their fate is thought to be constrained principally by their position. Cell fate is progressively restricted by localised signalling cues from areas including the primitive streak (PS). However, it is unknown whether this restriction accompanies, at the single cell level, a reduction in potency. Investigation of these early transition events in vitro is possible via the use of Epiblast Stem Cells (EpiSCs), self-renewing pluripotent cell lines equivalent to the postimplantation epiblast. Strikingly, EpiSCs express various early lineage-specific markers in self-renewing conditions. However, it is unknown whether cells that express these markers are pluripotent, spontaneously differentiated, or biased towards specific lineages. Here we show that EpiSC are inherently heterogeneous and contain two major and mutually exclusive subpopulations with PS and neural characteristics respectively. Using differentiation assays and embryo grafting we demonstrate that PS-like EpiSCs are biased towards mesoderm and endoderm differentiation but they still retain their pluripotent character. The acquisition of a PS character by undifferentiated EpiSC is mediated by paracrine Wnt signalling. Elevation of Wnt activity promotes further restriction into PS-associated cell fates which occurs via the generation of distinct clonal mesendodermal and neuromesodermal precursors. Collectively, our data suggest that primed pluripotency encompasses a range of reversible lineage-biased states reflecting the birth of pioneer lineage precursors from a pool of uncommitted EpiSCs similar to the earliest cell fate restriction events taking place in the gastrula-stage epiblast.
2014-03-04 | GSE48476 | GEO
Project description:During gastrulation, epiblast cells are pluripotent and their fate is thought to be constrained principally by their position. Cell fate is progressively restricted by localised signalling cues from areas including the primitive streak (PS). However, it is unknown whether this restriction accompanies, at the single cell level, a reduction in potency. Investigation of these early transition events in vitro is possible via the use of Epiblast Stem Cells (EpiSCs), self-renewing pluripotent cell lines equivalent to the postimplantation epiblast. Strikingly, EpiSCs express various early lineage-specific markers in self-renewing conditions. However, it is unknown whether cells that express these markers are pluripotent, spontaneously differentiated, or biased towards specific lineages. Here we show that EpiSC are inherently heterogeneous and contain two major and mutually exclusive subpopulations with PS and neural characteristics respectively. Using differentiation assays and embryo grafting we demonstrate that PS-like EpiSCs are biased towards mesoderm and endoderm differentiation but they still retain their pluripotent character. The acquisition of a PS character by undifferentiated EpiSC is mediated by paracrine Wnt signalling. Elevation of Wnt activity promotes further restriction into PS-associated cell fates which occurs via the generation of distinct clonal mesendodermal and neuromesodermal precursors. Collectively, our data suggest that primed pluripotency encompasses a range of reversible lineage-biased states reflecting the birth of pioneer lineage precursors from a pool of uncommitted EpiSCs similar to the earliest cell fate restriction events taking place in the gastrula-stage epiblast. Total RNA obtained (3 biological replicates) from flow sorted dsRed2+, dsRed2-, and +CHIRON treated for 48h cells was isolated and labelled/amplified using the IlluminaM-BM-. TotalPrepM-bM-^DM-" RNA Amplification Kit (Life Technologies)
2014-03-04 | E-GEOD-48476 | biostudies-arrayexpress