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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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			Action	DRS
	ERR5659860.fastq.gz	Fastqsanger.gz
	ERR5659870.fastq.gz	Fastqsanger.gz
	ERR5659861.fastq.gz	Fastqsanger.gz
	ERR5659871.fastq.gz	Fastqsanger.gz
	ERR5659862.fastq.gz	Fastqsanger.gz

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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

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

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

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

Epigenome analysis of hESCs undergoing neuronal differentiation

Project description:Genome wide DNA methylation profiling of human embryonic stem cells of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated towards neuronal cells for 13 days, and sampled for downstream analysis at day 0, 6, 10 and 13 . Cells exposed to 50, 100, 200 and 400 nM citalopram from Day 1 were charachterised at Day 6, 10 and 13. The Illumina Infinium MethylationEPIC_v-1-0_B3 was used to obtain DNA methylation profiles accross approximately 850k CpGs in differentiating cells.

2024-07-01 | GSE260890 | GEO

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