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Expression data from H9 human embryonic stem cells (hESCs) differentiated to Early Mesoendoderm

ABSTRACT: We used microarrays to detail the global programme of gene expression during early hESC differentiation to Mesendoderm using FBS.

ORGANISM(S): Homo sapiens

PROVIDER: GSE74004 | GEO | 2016/03/22

SECONDARY ACCESSION(S): PRJNA298727

REPOSITORIES: GEO

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Expression data from H9 human embryonic stem cells (hESCs) differentiated to Early Mesoendoderm

Project description:We used microarrays to detail the global programme of gene expression during early hESC differentiation to Mesendoderm using FBS. Samples of hESCs were taken at undifferentiated state (0h), 8h of differentiation, 24h of differentiation, and 72h of differentiation with three replicates (A, B, and C) at each time point.

2016-03-22 | E-GEOD-74004 | biostudies-arrayexpress

Expression data from H9 human embryonic stem cells (hESCs) infected with either lentiviral non-silencing shRNA or shRUNX1, and differentiated to early mesendoderm

Project description:We used microarrays to detail the global program of gene expression during early hESC differentiation to mesendoderm using FBS, with and without RUNX1 depletion.

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Genome-wide profile of 5-hydroxymethylcytosine (5-hmC) in H9 human embryonic stem cells (hESCs)

Project description:The link between single cell variation and population level fate choices lacks an explanation despite extensive observations of gene expression and epigenetic variation among individual cells. Here, we found that single human embryonic stem cells (hESCs) have different and biased differentiation potentials toward either neuroectoderm or mesendoderm depending on their G1 lengths before the onset of differentiation. Single cell variation in G1 length establishes a probability distribution in which increased variation biases stem cells toward neuroectoderm. Although sister stem cells generally share G1 lengths, a variable proportion of cells have asymmetric G1 lengths, which maintains the population dispersion. WNT levels control the G1 length distribution apparently as a means of priming the fate of hESC populations once they undergo differentiation. Global 5-hydroxymethylcytosine levels are regulated by G1 length and thereby link G1 length to differentiation outcomes of hESCs. Our findings suggest G1 length distribution links intra-population heterogeneity to population outcome.

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Expression data from human embryonic stem cells (hESCs) and Activin-induced/derived cells

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Expression data from human embryonic stem cells (hESCs) and Activin-induced/derived cells

Project description:Nodal/Activin signaling directs mesendoderm specification in early vertebrate embryogenesis. We have characterized transcriptional profiling of human embryonic stem cells and Activin-treated cells at different timepoints. In this dataset, we include the timecourse gene expression data obtained from hESC differentiation post Activin treatment, examining at day 0, 1, 3 and 5. Four biological replicates were used for day 0, three for day 1, three for day 3, and four for day 5. Cells were harvested and used for total RNA preparation using Trizol (Invitrogen). Gene expression was analyzed using GeneChip Human Exon 1.0 ST Array (Affymetrix).

2011-05-21 | E-GEOD-29421 | biostudies-arrayexpress

RNA-seq of retinal organoids differentiated from hESCs carrying mutations in the RB1 gene

Project description:hESC lines carrying deleterious mutations in the RB1 gene in heterozygous and homozygous state were generated by genome-editing based on CRISPR/Cas9. Parental cell line and genome-edited cell lines were differentiated into retinal organoids for 152 days based on the Protocol published by Döpper et al., Current protocols, PMID: 32956559. Briefly, single cells were reaggregated in presence of dual SMAD and WNT-inhibition; retinal tissue became visible from day 12 onward. BMP4-induction and addition of small molecules CHIR99021 and SU5402 directed differentiation towards retina and retinal pigment epithelium. Long-term differentiation was carried out in the presence of 10% FBS, taurine and retinoic acids. Organoids were collected at indicated time points and either embedded for cryosectioning and immunostaining or frozen at -80°C for RNA preparation.

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Sustained intrinsic WNT and BMP4 activation impairs hESC differentiation to definitive endoderm and drives the cells towards extra-embryonic mesoderm

Project description:This dataset includes the RNA sequencing of five replicates of the undifferentiated hESC subline VUB03_S2, which shows impaired mesendoderm induction, and 14 WT samples from GSE116372.

2021-04-06 | GSE134454 | GEO

RNAseq on WT and Meteor KO Embryonic Stem Cells and day3 differentiated cells

Project description:We have demonstrated that Meteor KO cells are associated with a global transcriptional reprogramming associated to a block of Mesendoderm specification. Meteor KO cells loses their developmental competence for Mesendoderm specification in pluripotency and are redirected to a neuroectoderm fate.

2017-10-10 | GSE103583 | GEO

Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) revealed genomic chromatin accessibilities change induced by loss of ARID1A in differentiated (day 4) H9 hESCs

Project description:We reported loss of ARID1A promoted neurogenesis and inhibited cardiogenesis. Under microscopy, we observed that spontaneously differentiated cells were induced in ARID1A KO H9 hESCs cultured in mTesR medium. We did not know what cells types were. Here ATAC-seq were used to investigate chromatin accessibilities change in differentiated (day 4) WT H9 hESCs and ARID1A KO hESC cells.

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RNA- and ATAC-seq data from hESCs differentiated with Wnt and Activin with or without CPI-203

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