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

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

PROVIDER: PRJEB44133 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5659998.fastq.gz	Fastqsanger.gz
	ERR5659999.fastq.gz	Fastqsanger.gz
	ERR5660000.fastq.gz	Fastqsanger.gz
	ERR5660010.fastq.gz	Fastqsanger.gz
	ERR5660001.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

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

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

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

Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts [ATAC-Seq]

Project description:ATAC-seq analysis revealed similarity/dissimilarity in chromatin accessibility between human blastocyst derived trophoblast stem cells (hbdTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs) compared with HFFs which underwent 3 days of ectopic expression of GATA3, OCT4, KLF4, MYC (GOKM) or OCT4, SOX2, KLF4 and MYC (OSKM).

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Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts [RRBS]

Project description:RRBS analysis revealed similarity/dissimilarity between human blastocyst derived trophoblast stem cells (hbdTSCs), human induced trophoblast stem cells (hiTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs, hiPSCs)

2023-02-21 | GSE182015 | GEO

Direct Induction of Trophoblast Stem Cells from Human Fibroblasts (RRBS)

Project description:Transcription profile analysis revealed similarity/dissimilarity between human blastocyst derived trophoblast stem cells (hbdTSCs), human induced trophoblast stem cells (hiTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs, hiPSCs)

2023-05-01 | GSE136599 | GEO

Direct Induction of Trophoblast Stem Cells from Human Fibroblasts (RNA-seq)

2023-05-01 | GSE136598 | GEO

Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts [RNA-Seq]

Project description:Transcription profile analysis revealed similarity/dissimilarity between human blastocyst derived trophoblast stem cells (hbdTSCss), human induced trophoblast stem cells (hiTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs, hiPSCs)

2023-02-21 | GSE182014 | GEO

Pluripotency-Independent Induction of Human Trophoblast Stem Cells from Fibroblasts [ChIP-Seq]

Project description:ChIP-seq analysis revealed similarity/dissimilarity in deposition of H3K4me2 histone mark between human blastocyst derived trophoblast stem cells (hbdTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs) compared with HFFs which underwent 3 days of ectopic expression of GATA3, OCT4, KLF4, MYC (GOKM) or OCT4, SOX2, KLF4 and MYC (OSKM).

2023-02-21 | GSE182013 | GEO

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