Genome-wide analysis of gene expression in human embryonic stem cells (hESCs) and their differentiated cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE36255 | GEO | 2012/12/31
SECONDARY ACCESSION(S): PRJNA153073
REPOSITORIES: GEO
Similar Datasets
Project description:In order to investigate the gene expression changes in human embryonic stem cells (hESCs) during differentiation, we performed a microarray analysis from RNAs isolated from undifferentiated hESCs and their differentiated cells incubated for 1 week or 2 weeks in ESC medium. Human SNUhES3 ESCs (Seoul National University Hospital, Seoul, Korea) were cultured on mitotically-arrested STO feeder cells (ATCC, Manassas, USA) in DMEM/F12 supplemented with 20% knockout serum replacement (KSR). The embryoid bodies were incubated for 1 or 2 weeks in the above ESC medium without bFGF. Cells were then lysed and RNA was isolated.
2012-12-31 | E-GEOD-36255 | biostudies-arrayexpress
Project description:The proteome of undifferentiated human embryonic stem cells (hESCs) was profiled by deep mass spectrometry-based proteomics of whole-cell extracts from suspension cultures of TE03 cells, in four biological replicates. This data accompanies the manuscript: "Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells". Abstract: "Embryonic stem cell (ESC) self-renewal and cell-fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that directly bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during exit from pluripotency and early lineage specification. Moreover, we show that nearly 200 RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly bound by this factor. Intriguingly, over 20 percent of the proteins detected in our study are putative DNA- and RNA-binding proteins (DRBPs), among them key transcription factors (TFs). Using fluorescently labeled RNA and seCLIP (single-end enhanced crosslinking and immunoprecipitation) experiments, we discover that the pluripotency-associated STAT3 and OCT4 TFs interact with RNA in hESCs and confirm the direct binding of STAT3 to the conserved NORAD long-noncoding RNA. Taken together, our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated, reinforcing the importance of post-transcriptional regulation in stem cell biology".
2023-05-05 | PXD025278 | Pride
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
Project description:Here, we performed RNA-interactome capture (RIC) on nuclear fractions from human embryonic stem cells (hESCs). The poly(A)+ RNA-bound proteome was determined by UV light-mediated cross-linking (CL) of RNAs to proteins in living cells, followed by nuclei isolation, oligo(dT) purification of poly(A)-RNA-protein complexes, and mass spectrometry analysis of captured proteins. As a control, we applied a similar strategy to non-cross-linked (non-CL) samples. RIC was performed in four independent biological replicates. This data accompanies the manuscript: "Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells". Abstract: "Embryonic stem cell (ESC) self-renewal and cell-fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that directly bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during exit from pluripotency and early lineage specification. Moreover, we show that nearly 200 RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly bound by this factor. Intriguingly, over 20 percent of the proteins detected in our study are putative DNA- and RNA-binding proteins (DRBPs), among them key transcription factors (TFs). Using fluorescently labeled RNA and seCLIP (single-end enhanced crosslinking and immunoprecipitation) experiments, we discover that the pluripotency-associated STAT3 and OCT4 TFs interact with RNA in hESCs and confirm the direct binding of STAT3 to the conserved NORAD long-noncoding RNA. Taken together, our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated, reinforcing the importance of post-transcriptional regulation in stem cell biology".
2023-05-05 | PXD025262 | Pride
Project description:Embryonic stem cell (ESC) self-renewal and cell-fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carried out a proteome-wide screen and identified 810 proteins that directly bind RNA in hESCs. We determined the RBP catalog by using RNA-interactome capture (RIC), a method based on UV light-mediated cross-linking (CL) of RNAs to proteins in living cells, followed by oligo(dT) purification of poly(A)-RNA-protein complexes and mass spectrometry analysis of captured proteins. As control, we applied a similar strategy to non-cross-linked (non-CL) samples. To uncover the identity of the eluted proteins, we performed in-solution tryptic digestion of CL and non-CL eluates and analyzed their contents by a high-resolution mass spectrometer (Q-Exactive Plus). We then performed differential proteome analysis between CL and non-CL eluates, resulting in a set of 810 high-confidence protein groups, defined as the hESC RNA-interactome. RIC was carried out in four independent biological replicates. This data accompanies the manuscript: "Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells".
2023-05-05 | PXD025194 | Pride
Project description:Mass spectrometry analysis was carried out to investigate the protein expression landscape of RNA-binding proteins (RBPs) during a time-course of spontaneously differentiating human embryonic stem cells (hESCs). Mass spectrometry was performed on whole-cell extracts of differentiating TE03 (I3) hESCs at four time-points (days 0, 23, 39, and 54), each with two biological replicates.
2023-05-05 | PXD025274 | Pride
Project description:Several of the essential core transcriptional control elements in human embryonic stem cells (ESCs) have been identified, but the production and function of alternative isoforms in self-renewal, pluripotency and tissue lineage specification remain largely unknown. We have modified the H9 ESC line to allow for drug selection of human pluripotent ESCs and cardiac progenitors. Exon-level microarray expression data from undifferentiated ESCs and day 40 cardiac precursors were used to identify differentially expressed and alternative splice isoforms during differentiation. Keywords: comparison RNA from a homogenous population of undifferentiated hESCs (REX1-neo promoter drug selection) and differentiated day 40 cardiomyocytes (alpha MHC-puro promoter drug selection) was isolated and profiled with exon-tiling arrays.
2008-10-24 | E-GEOD-13297 | biostudies-arrayexpress
Project description:Here, we used high-resolution mass spectrometry to identify differentially expressed RNA-binding proteins (RBPs) between TE03 (I3) human embryonic stem cells (hESCs) and human foreskin fibroblasts (HFFs). 2102Ep embryonal carcinoma (EC) cells were used as a reference for pluripotent cells. This data accompanies the manuscript: "Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells". Abstract: "Embryonic stem cell (ESC) self-renewal and cell-fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that directly bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during exit from pluripotency and early lineage specification. Moreover, we show that nearly 200 RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly bound by this factor. Intriguingly, over 20 percent of the proteins detected in our study are putative DNA- and RNA-binding proteins (DRBPs), among them key transcription factors (TFs). Using fluorescently labeled RNA and seCLIP (single-end enhanced crosslinking and immunoprecipitation) experiments, we discover that the pluripotency-associated STAT3 and OCT4 TFs interact with RNA in hESCs and confirm the direct binding of STAT3 to the conserved NORAD long-noncoding RNA. Taken together, our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated, reinforcing the importance of post-transcriptional regulation in stem cell biology".
2023-05-05 | PXD025284 | Pride
Project description:To detect the effect of early culture on hESCs, almost all initial-passaged hESCs have normal expression of DLK1-DIO3 gene cluster, the low-passaged hESCs lost the expression of DLK1-DIO3 gene cluster.
2014-06-30 | GSE38662 | GEO
Project description:Many studies have compared the genetic and epigenetic profiles of human induced pluripotent stem cells (hiPSCs) to human embryonic stem cells (hESCs) and yet the picture remains unclear. To address this, we derived a population of neural precursor cells (NPCs) from the H1 (WA01) hESC line and generated isogenic iPSC lines by reprogramming. The gene expression and methylation profile of three lines were compared to the parental line and intermediate NPC population. We found no gene probe with expression that differed significantly between hESC and iPSC samples under undifferentiated or differentiated conditions. Analysis of the global methylation pattern also showed no significant difference between the two PSC populations. Both undifferentiated populations were distinctly different from the intermediate NPC population in both gene expression and methylation profiles. One point to note is that H1 is a male line and so extrapolation to female lines should be cautioned. However, these data confirm our previous findings that there are no significant differences between hESCs and hiPSCs at the gene expression or methylation level. 22 samples: 1 human NPC, 2 human ESC (UNDIFF), 5 human iPSC (UNDIFF), 2 human ESC (EB_ecto), 5 human iPSC (EB_ecto), 2 human ESC (EB_mesend), 5 human iPSC (EB_mesend)
2014-01-01 | E-GEOD-51561 | biostudies-arrayexpress