Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-seq of H9 nEnd cells subjected to mesoderm differentiation.

ABSTRACT: The origin of human extraembryonic mesoderm (ExM) has been heavily debated. In order to address if ExM can be derived from primitive endoderm (PrE), we treated the human PrE cell line (also called na�ve extraembryonic endoderm (nEnd)) with a mesoderm induction protocol and sequenced the entire day 15 cell population.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Karin Farkas

PROVIDER: E-MTAB-12562 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA-seq of hESC-derived, differentiating cardiac cells on day 2, 3 and 8; control and PD0325901-treated.

Project description:The role of FGF-MEK-ERK signalling pathway during embryonic heart development has not been fully elucidated. Here, we inhibited the pathway for 1 day using PD0325901, a MEK inhibitor, at the lateral plate mesoderm stage during cardiac differentiation of human embryonic stem cells. Cells were collected on day 2 (before PD0325901 administration), day 3 and day 8 to determine the effect of a transient FGF-MEK-ERK pathway modulation on the cardiac cell fate choice.

2023-06-28 | E-MTAB-12619 | biostudies-arrayexpress

mRNA expression data from differentiation of human ESCs into definitive endoderm, Cyt49 on matrigel

Project description:hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm derived tissues: pancreas, liver, gut, lung. We used microarrays to detail the changes in mRNA expression during the transition from pluripotent hESCs into definitive endoderm. hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0, day 2 and day 4.

2010-07-30 | E-GEOD-16681 | biostudies-arrayexpress

MicroRNA expression data from differentiation of human H9 ESCs into definitive endoderm on MEF feeder layers

Project description:Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm. hESCs (H9) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0 (hESCs), and day 4 (DE).

2010-07-30 | E-GEOD-16689 | biostudies-arrayexpress

MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm on MEF feeder layers

Project description:Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung) We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE. formation. Samples were collected at day 0 (hESCs), and day 4 (DE).

2010-07-30 | E-GEOD-16687 | biostudies-arrayexpress

MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm in feeder-free conditions

Project description:Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm. hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0 (2 samples), day 2 (3 samples) and day 4 (3 samples).

2010-07-29 | E-GEOD-16678 | biostudies-arrayexpress

Transcription profiling by array of human embryonic stem cells over-expression SOX7 and SOX17

Project description:This study aimed to understand the transcriptional networks regulating endoderm specification from HESC and therefore explored the phenotype of CA1 and CA2 HESC constitutively over-expressing SOX7 or SOX17. Cell lines were created using an inducible construct whereby clonal populations containing transgene integration are selected by Neomycin resistance without expressing of the gene of interest (NoCre controls). Transgene expression is induced via Cre-mediated recombination and selected for puromycin resistance (SOX O/E). The phenotype of the resulting cells suggests that SOX7 expressing HESC represent stable extraembryonic endoderm progenitors, while SOX17 expressing HESC represent early definitive endoderm progenitors. Both in vitro and in vivo SOX7 expressing HESC are restricted to the extraembryonic endoderm lineage, while SOX17 expressing HESC demonstrate mesendodermal specificity. In vitro, SOX17 expressing HESC efficiently produce mature definitive endoderm derivatives. The molecular phenotype of the resulting SOX7 and SOX17 expressing HESC was characterized by microarray analysis Experiment Overall Design: Total RNA was extracted from confluent monolayer cultures of SOX7 over-expressing HESC, SOX17 over-expressing HESC, and their respective control parental HESC lines (designated NoCre Sox7 and NoCre Sox17).

2008-10-20 | E-GEOD-10809 | biostudies-arrayexpress

RNA-seq of H9 cell line during differentiation from naïve extraembryonic endoderm to extraembryonic mesoderm.

Project description:Extraembryonic mesoderm (ExM) is one of the first cell types that emerges during embryogenesis and constitutes essential supportive tissues for the pregnancy. Primate ExM is known to form prior to gastrulation, unlike its murine counterpart which is derived from the primitive streak. Based on the embryonic morphology and the proximity of ExM to the extraembryonic endoderm (hypoblast), we hypothesised that ExM can be derived in vitro from the naïve extraembryonic endoderm (nEnd) cell line. We applied a mesoderm differentiation protocol, which has been reported to induce ExM from mouse epiblast stem cells, on human nEnd and analysed the transcriptome on day 0, 1, 2, 8 and 15.

2023-06-29 | E-MTAB-12517 | biostudies-arrayexpress

Gata6 potently initiates reprogramming of pluripotent and differentiated cells to extraembryonic endoderm stem cells [time-course microarray]

Project description:Transcription factor-mediated reprogramming is a powerful method to study cell fate changes. In this work, we demonstrate that the transcription factor Gata6 can initiate reprograming of multiple cell types to induced extraembryonic endoderm (iXEN) cells. Intriguingly, Gata6 is sufficient to drive iXEN cells from mouse pluripotent cells and differentiated neural cells. Furthermore, GATA6 induction in human ES (hES) cells also downregulates pluripotency gene expression and upregulates extraembryonic endoderm genes, revealing a conserved function in mediating this cell fate switch. Profiling transcriptional changes following Gata6 induction in mES cells reveals step-wise pluripotency factor disengagement, with initial repression of Nanog and Esrrb, then Sox2 and finally Oct4, alongside step-wise activation of extraembryonic endoderm genes. Chromatin immunoprecipitation and subsequent high-throughput sequencing analysis shows Gata6 enrichment near both pluripotency and endoderm genes, suggesting that Gata6 functions as both a direct repressor and activator. Together this demonstrates that Gata6 is a versatile and potent reprogramming factor that can act alone to drive a cell fate switch from diverse cell types. Time-course microarray analysis of Gata6-mediated reprogramming from 12 to 144 hours of doxycycline treatment in mouse embryonic stem (mES) cells compared to uninduced mES cells, embryo-derived extraembryonic endoderm (XEN) cells and Sox7 overexpressing mES cells after 144 hours of doxycycline treatment.

2015-06-30 | E-GEOD-69321 | biostudies-arrayexpress