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RNA-Seq of 3iL human embryonic stem cells

ABSTRACT: Human embryonic stem cells (hESCs) are isolated from the inner cell mass of the blastocysts. The pluripotent properties of hESCs enable the derivation of cell-types or tissues of different lineages for potential applications such as therapeutics discovery and regenerative medicine. Even though hESCs are pluripotent, differences have been observed when compared to the native pluripotent epiblast cells of the blastocyst. We use a chemical approach (3iL: 3 small molecule inhibitor and cytokine) to induce an expression signature that more closely resembles native pluripotent cells. To better understand the difference between this hESC state and the conventional hESC state, we generated the global expression profiles using RNA-seq.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Jonathan Goke

PROVIDER: E-MTAB-2031 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Induction of a human pluripotent state with distinct regulatory circuitry that resembles preimplantation epiblast.

Chan Yun-Shen YS Göke Jonathan J Ng Jia-Hui JH Lu Xinyi X Gonzales Kevin Andrew Uy KA Tan Cheng-Peow CP Tng Wei-Quan WQ Hong Zhong-Zhi ZZ Lim Yee-Siang YS Ng Huck-Hui HH

Cell stem cell 20131201 6

Human embryonic stem cells (hESCs) are derived from the inner cell mass of the blastocyst. Despite sharing the common property of pluripotency, hESCs are notably distinct from epiblast cells of the preimplantation blastocyst. Here we use a combination of three small-molecule inhibitors to sustain hESCs in a LIF signaling-dependent hESC state (3iL hESCs) with elevated expression of NANOG and epiblast-enriched genes such as KLF4, DPPA3, and TBX3. Genome-wide transcriptome analysis confirms that th ...[more]

PMID: 24315441

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ChIP-Seq of Histone Modifications in 3iL Human Embryonic Stem Cells

Project description:Human embryonic stem cells (hESCs) are isolated from the inner cell mass of the blastocysts. The pluripotent properties of hESCs enable the derivation of cell-types or tissues of different lineages for potential applications such as therapeutics discovery and regenerative medicine. Even though hESCs are pluripotent, differences have been observed when compared to the native pluripotent epiblast cells of the blastocyst. We use a chemical approach (3iL: 3 small molecule inhibitor and cytokine) to induce an expression signature that more closely resembles native pluripotent cells. This experiment is the epigenetic data of the study.

2013-12-05 | E-MTAB-2041 | biostudies-arrayexpress

ChIP-Seq of OCT4, NANOG, p300 in 3iL Human Embryonic Stem Cells

2013-12-05 | E-MTAB-2044 | biostudies-arrayexpress

ChIP-Seq of STAT3 in 3iL Human Embryonic Stem Cells

2013-12-05 | E-MTAB-2042 | biostudies-arrayexpress

ChIP-seq of H1 human embryonic stem cells (hESCs) to map the global binding profile of EZH2 to investigate the association of PRDM14 binding with the PRC2 in hESCs

Project description:An experiment was performed to map the global binding profile of EZH2 in human embryonic stem cells (hESCs). How the Polycomb Repressive Complex 2 (PRC2) is recruited to the DNA in hESC remains largely unknown. Previous studies on the transcription factor PRDM14 suggested that PRDM14 plays a repressive role in hESCs. Here, we mapped the global binding profile of EZH2 in hESC to investigate the association of PRDM14 binding with the PRC2 in hESCs. EZH2 binding is found to be enriched in PRDM14 binding sites. The PRC2 dependent repressive role of PRDM14 is further supported by the strong correlation of PRDM14 binding with the repressive histone modification H3K27me3.

2012-11-01 | E-MTAB-1305 | biostudies-arrayexpress

A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells

Project description:We compared hESCs with their neuronal counterpart to quantify differences in the expression of cold-shock domain containing proteins. While the transcriptional network of human embryonic stem cells (hESCs) has been extensively studied, relatively little is known about how post-transcriptional modulations determine hESC function. RNA-binding proteins play central roles in RNA regulation, including translation and turnover. Here we show that the RNA-binding protein CSDE1 is highly expressed in hESCs to maintain their undifferentiated state and prevent default neural fate. Notably, loss of CSDE1 accelerates neural differentiation and potentiates neurogenesis. Conversely, ectopic expression of CSDE1 impairs neural differentiation. We find that CSDE1 post-transcriptionally modulates core components of multiple regulatory nodes of hESC identity, neuroectoderm commitment and neurogenesis. Among these key pro-neural/neuronal factors, CSDE1 binds fatty acid binding protein 7 (FABP7) and vimentin (VIM) mRNAs as well as transcripts involved in neuron projection development regulating their stability and translation. Thus, our results uncover CSDE1 as a central post-transcriptional regulator of hESC identity and neurogenesis.

2018-05-16 | PXD007738 | Pride

Genome Wide Profiling of p53 Response to Differentiation or DNA Damage of Human Embryonic Stem Cells

Project description:Tumor suppressor p53 promotes differentiation of human embryonic stem cells (hESCs), but an in-depth understanding of mechanism is lacking. Here, we define p53 functions in hESCs by genome wide profiling of p53 chromatin interactions and intersection with gene expression during early differentiation and in response to DNA damage. During differentiation, p53 targets and regulates a unique collection of genes, many of which encode transcription factors and developmental regulators with chromatin structure poised by OCT4 and NANOG and marked by repressive H3K27me3 in pluripotent hESCs. In contrast, genes associated with cell migration and motility are bound by p53 specifically after DNA damage. Surveillance functions of p53 in regulation of cell death and cell cycle genes are conserved during both DNA damage and differentiation. Our findings expand the registry of p53 -regulated genes in hESCs and define specific functions of p53 in opposing pluripotency, which are highly distinct from stress-induced p53 response in stem cells. Identification of p53 binding sites in hESC under three conditions: Pluripotent, DNA damaged, Differentiating

2013-10-18 | E-GEOD-39762 | biostudies-arrayexpress

Genome Wide Profiling of p53 Response to Differentiation or DNA Damage of Human Embryonic Stem Cells

2013-10-18 | E-GEOD-39912 | biostudies-arrayexpress

Comparative analysis from hESC from different developmental sources of derivation

Project description:Whole genome expression analysis reveals that single blastomeres from day-3 human embryos and blastocysts show unique gene signature, thus hESC derived from these two developmental sources might show differential gene expression profile. Comparative gene expression analysis has revealed that no significant differences exist between hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental progression. hESC derived from single blastomeres (VAL-10B and VAL-11B) and from ICM (VAL-5, -7, and -8) were compared by global gene expression

2012-11-27 | E-GEOD-42520 | biostudies-arrayexpress

A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells

Project description:While the transcriptional network of human embryonic stem cells (hESCs) has been extensively studied, relatively little is known about how post-transcriptional modulations determine hESC function. RNA-binding proteins play central roles in RNA regulation, including translation and turnover. Here we show that the RNA-binding protein CSDE1 is highly expressed in hESCs to maintain their undifferentiated state and prevent default neural fate. Notably, loss of CSDE1 accelerates neural differentiation and potentiates neurogenesis. Conversely, ectopic expression of CSDE1 impairs neural differentiation. We find that CSDE1 post-transcriptionally modulates core components of multiple regulatory nodes of hESC identity, neuroectoderm commitment and neurogenesis. Among these key pro-neural/neuronal factors, CSDE1 binds fatty acid binding protein 7 (FABP7) and vimentin (VIM) mRNAs as well as transcripts involved in neuron projection development regulating their stability and translation. Thus, our results uncover CSDE1 as a central post-transcriptional regulator of hESC identity and neurogenesis.

2018-05-16 | PXD007270 | Pride

Untargeted histone profiling of human embryonic stem cell conversion over time reveals fundamental epigenetic changes between pluripotent and naive states

Project description:Recently, various groups managed to isolate naïve human embryonic stem cell (hESC) state in vitro has come into acceptance. However, a thorough epigenetic characterization of this human ground state, defined as a state without any epigenetic restrictions, and how that compares to mouse is currently lacking. Also, the epigenomic remodeling required to obtain the ground state, and the important transient processes occurring during the remodeling, have remained elusive in human. Here, we address these issues by using an untargeted mass spectrometry-based (MS) approach to profile the histone epigenome in a time-resolved experimental design. Special care was given to defining the naïve hESC state that was reached over 12 passages (P12, 37 days) in feeder-free conditions in this study. We found that conversion is a multi-staged process with a prominent cellular disturbance after stimulation (P3), an increase in cell proliferation between P3 and P6 and a naïve cell state stabilizing between P9 and P12. In total, 20 different histone post-translational modifications (hPTMs) changed significantly over time from primed to naïve hESCs. Most notably, H3K27me3 is the most prominently increasing hPTM in naïve hESCs, in line with what we recently described in mouse. Essentially, we present a first roadmap of the changing human histone epigenome from primed to naïve state and emphasize that the overlap with mouse hints at a conserved Mammalian epigenetic signature of the ground state.

2019-11-27 | PXD013067 | Pride

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