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Time-course RNA-seq analysis of spontaneously differentiating TE03 human embryonic stem cells (hESCs)

ABSTRACT: Time-course RNA-Seq analysis of spontaneously differentiating TE03 (I3) human embryonic stem cells (hESCs)

PROVIDER: PRJEB44122 | ENA |

REPOSITORIES: ENA

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Time-course proteomic analysis of spontaneously differentiating human embryonic stem cells (hESCs)

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

Mass spectrometry based-proteomic analysis comparing the abundance of RNA-binding proteins (RBPs) between TE03 (I3) human embryonic stem cells (hESCs) and human foreskin fibroblasts (HFFs)

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

Transcriptome profiling of TE03 (I3) human embryonic stem cells (hESCs) by paired-end RNA-Sequencing

Project description:Transcriptome profiling of TE03 (I3) human embryonic stem cells (hESCs) by paired-end RNA-Sequencing

| PRJEB44131 | ENA

11-Point Time Course Study of Differentiating J1 Embryoid Bodies

Project description:An 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days. Keywords: Time course

2005-12-06 | GSE3749 | GEO

BRACHYURY knockdown in differentiating hESCs

Project description:Transcriptional profiling of H9 hESCs (wild type and BRACHYURY shRNA knockdown) differentiated for 36h or 72h in chemically-defined culture media supplemented with FGF2, LY294002 and either BMP4 or ActivinA.

2015-05-19 | E-MTAB-2912 | biostudies-arrayexpress

Deep proteomic profiling of TE03 (I3) human embryonic stem cells (hESCs)

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

LIN28 eRIP in Differentiating hESCs

Project description:Excluded-volume-effect-optimized RNA-IP (eRIP) of LIN28-associated mRNAs in H1 hESCs. H1s are induced to differentiate into either trophoblast (TE) or neural (N) lineages, and LIN28 eRIP performed at 0hr (Undifferentiated), 12hr TE, 24hr TE and 24hr N

2014-07-21 | E-MTAB-1652 | biostudies-arrayexpress

RNA-sequencing analysis comparing the expression of RNA-binding proteins (RBPs) between TE03 (I3) human embryonic stem cells (hESCs) and human foreskin fibroblasts (HFFs)

Project description:RNA-sequencing analysis comparing gene expression between TE03 (I3) human embryonic stem cells (hESCs) and human foreskin fibroblasts (HFFs)

| PRJEB44133 | ENA

seCLIP-Seq (single-end enhanced crosslinking and immunoprecipitation) of STAT3, OCT4, and SRSF1 in human embryonic stem cells (hESCs)

Project description:seCLIP-Seq (single-end enhanced crosslinking and immunoprecipitation) of STAT3, OCT4, and SRSF1 in TE03 (I3) human embryonic stem cells (hESCs)

| PRJEB44137 | ENA

Comparison non-targeting hRNA hESCs versus UBE2K shRNA hESCs

Project description:Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. When compared with their differentiated counterparts, immortal human embryonic stem cells (hESCs) have a unique chromatin architecture and low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess a link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of UBE2K, a ubiquitin-conjugating enzyme. Loss of UBE2K increases the levels of H3K9 trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Concomitantly, loss of UBE2K impairs the ability of hESCs to differentiate into neural progenitors with neurogenic properties. Besides H3K9 trimethylation, we find that UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates both histone H3 levels and H3K9 trimethylation in C. elegans germline. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells.

2020-06-01 | PXD018625 | Pride

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