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RNA-Seq after knockdown of SON in human embryonic stem cells

ABSTRACT: RNA-Seq after knockdown of SON in human embryonic stem cells

PROVIDER: PRJEB4007 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR296095_1.fastq.gz	Fastqsanger.gz
	ERR296095_2.fastq.gz	Fastqsanger.gz
	ERR296096_1.fastq.gz	Fastqsanger.gz
	ERR296096_2.fastq.gz	Fastqsanger.gz
	ERR296097_1.fastq.gz	Fastqsanger.gz

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RNA-Seq after knockdown of SON in human embryonic stem cells

Project description:Human embryonic stem cells (hESCs) harbor the ability to undergo lineage-specific differentiation into clinically relevant cell types. Transcription factors and epigenetic modifiers are known to play important roles in the maintenance of pluripotency of hESCs. However, little is known about regulation of pluripotency through splicing. In this study, we identify the spliceosome-associated factor SON as a novel factor essential for the maintenance of hESCs. Depletion of SON in hESCs results in the loss of pluripotency and cell death. Using genome-wide RNA profiling, we identified transcripts that are regulated by SON. Importantly, we confirmed that SON regulates the proper splicing of transcripts encoding for pluripotency regulators such as PRDM14, OCT4, E4F1 and MED24. Furthermore, we show that SON is bound to these transcripts in vivo. In summary, we connect a splicing-regulatory network for accurate transcription production to the maintenance of pluripotency and self-renewal of hESCs.

2013-08-29 | E-MTAB-1687 | biostudies-arrayexpress

Son KD in mouse embryonic stem cells

Project description:Son KD in mouse embryonic stem cells

| PRJNA1128624 | ENA

Son KD in mouse embryonic stem cells

Project description:Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Resulting from a previous screen, the protein SON was identified as a potential noise regulator. We perform Son KD and utilize single-cell RNA sequencing (scRNA-seq) to quantify the changes in mean/noise of all transcripts. This dataset corresponds to the aforementioned scRNA-seq experiment upon Son KD.

2024-08-05 | GSE270846 | GEO

Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

2018-08-02 | MSV000082680 | GNPS

SON controls mouse early embryonic development by regulating RNA splicing and histone methylation

Project description:Thousands of genes are activated at later 2-cell embryos, which means that numerous pre-mRNAs are generated during this time. These pre-mRNAs must be accurately spliced to ensure that the mature mRNAs are translated to functional proteins. However, little is known about the roles of pre-mRNA splicing and cellular factors modulating pre-mRNA splicing during early embryonic development. Here, we report that downregulation of SON, a large Ser/Arg (SR)-related protein, reduced embryonic development and caused deficient blastomere cleavage. These embryonic developmental defects resulted from dysregulated nuclear speckle organization and pre-mRNA splicing of a set of cell-cycle-related genes. Furthermore, SON downregulation disturbed the transcriptome (2128 upregulation and 1399 downregulation) in 4-cell embryos. Increased H3K4me3, H3K9me3 and H3K27me3 levels were found in 4-cell embryos after SON downregulation. Taken together, those results demonstrate that accurate pre-mRNA splicing is essential for early embryonic development, and SON plays important roles on nuclear speckle organization, pre-mRNA splicing, the transcriptome establishment and histone methylation reprogramming during early embryonic development.

2025-07-31 | GSE273029 | GEO

Son Maintains Accurate Splicing of Pre-mRNAs Encoding Chromatin Modifiers

Project description:Exon and expression analysis of HeLa cells after knockdown of SON Serine-arginine-rich (SR) proteins play a key role in alternative pre-mRNA splicing in eukaryotes. Our laboratory recently showed that a large SR protein called Son has unique repeat motifs that are essential for maintaining the subnuclear organization of pre-mRNA processing factors in nuclear speckles. Motif analysis of Son highlights putative RNA interaction domains that suggest a direct role for Son in pre-mRNA splicing. A genome-wide screen was performed to identify putative human transcription and splicing targets of Son.

2011-12-22 | GSE28672 | GEO

OCT4 Knockdown in human embryonic stem cells

Project description:We studied the genomic locations of three key regulatory proteins (OCT4, NANOG and CTCF) in human and mouse embryonic stem (ES) cells [see Series GSE20650]. To identify the conserved and unique human OCT4 targets, we performed an OCT4 RNAi knock-down experiment. We find that species-specific transposable elements have profoundly altered the transcriptional circuitry of pluripotent stem cells. To identify the mRNA targets of OCT4: 12 samples were collected in total. Each sample is done in triplicate and samples were collected at 2 different time point, 2 days and 3 days after transfection. Luciferase knockdown serves as negative control and OCT4 knockdown is the experimental sample.

2010-04-13 | E-GEOD-21135 | biostudies-arrayexpress

Son Maintains Accurate Splicing of Pre-mRNAs Encoding Chromatin Modifiers

2011-12-22 | E-GEOD-28672 | biostudies-arrayexpress

Expression data from HeLa cells transiently transfected with control siRNA or SON siRNA

Project description:SON is a large Ser/Arg (SR)-related protein localized in nuclear speckles. SON siRNA causes defects in mitotic progression and genome instability. We used microarrays to detail the pattern of gene expression after SON knockdown. HeLa cells were grown in 100 mm dishes and transfected with negative control siRNA or SON siRNA (400 pmol). Then, cells were harvested after 66 hours and RNAs were isolated. Microarrays were performed using GeneChip Human Genome U133A 2.0 (Affymetrix).

2011-04-01 | E-GEOD-26888 | biostudies-arrayexpress

Label-free quantitative analysis proteomic profiles of human embryonic stem cell derived exosomes

Project description:In order to investigate the characteristics and mechanisms of embryonic stem cell derived exosomes attenuates transverse aortic constriction induced ventricular remodeling, the proteomic profiles of human embryonic stem cell derived exosomes were analysed by label-free quantification.

2020-12-10 | PXD023105 |

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