Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Total RNA-seq and long-read RNAseq (Nanopore) upon Son KD in mouse embryonic stem cells

ABSTRACT: 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 (1) total RNA sequencing (RNA-seq) to analyze differences in splicing efficiency of introns upon Son KD; and (2) Nanopore sequencing to analyze changes in isoform usage. These datasets correspond to the aforementioned total RNA-seq and long-read polyA+ cDNA Nanopore sequencing upon Son KD.

ORGANISM(S): Mus musculus

PROVIDER: GSE271659 | GEO | 2024/08/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Nanopore sequencing of UNC13A from SHSY5Y and patient RNA

Project description:UNC13A contains a novel cryptic exon which is expressed upon TDP-43 knockdown. However, it also features TDP-43 regulated intron retention of a downstream intron. To investigate the correlation of these two events, we performed Nanopore sequencing of amplicons from SHSY5Y cells with inducible TDP-43 knockdown, and FTD patient RNA samples

2022-02-10 | E-MTAB-11244 | biostudies-arrayexpress

Tubercidin treatment 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, a possible role of nuclear speckles in noise regulation was highlighted. We utilize tubercidin treatment and single-cell RNA sequencing (scRNA-seq) to quantify the changes in mean/noise of all transcripts upon nuclear speckle disruption. This dataset corresponds to the aforementioned scRNA-seq experiment upon tubercidin treatment.

2024-08-05 | GSE271082 | GEO

RNAseq identifies differentially expressed genes upon SON overexpression in WT and Mettl3 cKO LSK cells

Project description:The goal of this study is to identify gene expression changes upon SON overexpression in WT and Mettl3 cKO LSK (Lin-cKit+Sca1+) cells

2023-12-07 | GSE231637 | 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

Son Maintains Accurate Splicing of Pre-mRNAs Encoding Chromatin Modifiers

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

Translation inhibition with CHX 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? Our integrative approach, combining single-cell RNA sequencing with proteomics and regulator enrichment analysis, reveals 32 putative noise regulators. The approach utilizes global translation inhibition (i.e., potential protein regulators), and single-cell RNA sequencing (scRNA-seq) to quantify the changes in noise of all transcripts (i.e., potential mRNA targets). This dataset corresponds to the aforementioned scRNA-seq experiment upon translation inhibition with cycloheximide.

2024-08-05 | GSE271660 | GEO

single cell RNAseq identifies differential expressed genes upon SON overexpression in WT and Mettl3 cKO LSK cells

Project description:The goal of this study is to identify gene expression changes upon SON overexpression in WT and Mettl3 cKO LSK (Lin-cKit+Sca1+) cells at single cell level

2023-12-07 | GSE231863 | GEO

The SON splicing factor is required for intracellular trafficking that promotes centriole assembly

Project description:Control of the number of centrosomes is critical for cell division, trafficking and cilia. Regulation of centrosome number occurs through the precise duplication of centrioles that reside in the center of centrosomes. Here we explored transcriptional control of centriole assembly by focusing on alternative splicing factors in isolation from other cell cycle processes. Of five splicing factors originally identified as required for centriole assembly, only SON is specifically required. Procentriole assembly is severely disrupted when SON is reduced but early centriole assembly events still occur. Whole genome mRNA sequencing identified thousands of genes whose splicing and expression are affected by the reduction of SON, with an enrichment of genes involved in the microtubule cytoskeleton. SON is required for the proper splicing and expression of the centriolar satellite protein, CEP131. Fluorescence microscopy and electron tomography establish key differences to the trafficking and microtubule network around the centrosomes that contribute to the centriole assembly defects. This establishes SON as required for centriole assembly, partially through its activity in splicing CEP131 and through control of microtubules organized by the centrosome.

2021-12-22 | GSE164278 | GEO

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.

2011-04-01 | GSE26888 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data