Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation, modulates translation and spliceosomal processes

ABSTRACT: In this study we provide the gene expression profiles and MISO analyses for alternative splicing events such as exon skipping in wildtype versus OGFOD1 (oxoglutarate, glucose and iron dependent protein 1)-knock-out iPSC-derived cardiomyocytes, we further compare the profiles to wildtype which were treated with a drug inhibiting α-ketoglutarate-dependent hydroxylases (dimethyloxalylglycine) versus vehicle control. Altered translation and splicing processes play a role in differentiation processes and have been shown to be involved in disease progression in e.g. heart failure. OGFOD1 is a ribosomal prolyl-hydroxylase and which influences translation, here we show its further importance in cardiac differentiation and alternative splicing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE130521 | GEO | 2019/07/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes

Project description:In this study we report the gene expression profile and MISO analysis for alternative splicing events such as exon skipping in iPSC-derived cardiomyocytes which were treated with a drug inhibiting α-ketoglutarate-dependent hydroxylases (dimethyloxalylglycine) and compared to vehicle control. α-ketoglutarate-dependent hydroxylase inhibition plays a central role in cardiac hypoxia and the goal of this study was to identify new pathways in hypoxia beyond HIF-1α.

2016-05-05 | GSE71560 | GEO

OGFOD1 Regulates Translation to Alter Hypertrophy Susceptibility

Project description:Cardiac hypertrophy, a precursor for heart failure, requires increased translation. However, little is known of the mechanisms that regulate translation in hypertrophy. Members of the 2-oxoglutarate-dependent dioxygenase family regulate several aspects of gene expression, including translation. An important member of this family is OGFOD1. Here, we show OGFOD1 accumulates in failing human hearts. Upon OGFOD1 deletion, murine hearts showed transcriptomic and proteomic changes, with only 21 factors (0.6%) changing in the same direction at both the mRNA and protein levels. Additionally, OGFOD1-KO mice were protected from induced hypertrophy, supporting a role for OGFOD1 in the cardiac response to chronic stress.

2023-11-10 | GSE217755 | GEO

Analysis and design of RNA sequencing experiments for identifying mRNA isoform regulation

Project description:Through alternative splicing, most human genes express multiple isoforms that may have distinct or even antagonistic functions. To infer isoform regulation based on data from high-throughput sequencing of cDNA fragments (RNA-Seq), we have developed MISO, a computational model that estimates the expression level of alternatively spliced exons and mRNA isoforms and provides intuitive measures of con?dence in these estimates. Incorporation of the length distribution of inserted cDNA fragments in paired-end RNA-Seq analysis in MISO enables dramatic improvements in estimation of alternative splicing levels relative to previous methods. We show that one lane of paired-end RNA-Seq data can provide far more information about splicing than two lanes of single-end data, depending critically on properties of the distribution of cDNA fragment lengths in the sequenced library. MISO also leads to an intuitive method to detect di?erentially regulated exons or isoforms. Application of this method implicates the RNA splicing factor hnRNP H in regulation of alternative cleavage and polyadenylation, a role that is supported by UV crosslinking/immunoprecipitation/high-throughput sequencing (CLIP-Seq) analysis. Together, our results provide a probabilistic framework for RNA-Seq analysis, derive functional insights into pre-mRNA processing, and yield guidelines for the optimal design of RNA-Seq experiments for studies of gene and isoform expression. CLIPseq of hnRNP H in HEK 293T cells. RNAseq of polyA+ RNA from C2C12 mouse myoblasts stably expressing an empty vector or a vector containing an shRNA against CUGBP1. Libraries of two different insert lengths were created and examined.

2010-11-07 | E-GEOD-23694 | biostudies-arrayexpress

Analysis and design of RNA sequencing experiments for identifying mRNA isoform regulation

Project description:Through alternative splicing, most human genes express multiple isoforms that may have distinct or even antagonistic functions. To infer isoform regulation based on data from high-throughput sequencing of cDNA fragments (RNA-Seq), we have developed MISO, a computational model that estimates the expression level of alternatively spliced exons and mRNA isoforms and provides intuitive measures of conﬁdence in these estimates. Incorporation of the length distribution of inserted cDNA fragments in paired-end RNA-Seq analysis in MISO enables dramatic improvements in estimation of alternative splicing levels relative to previous methods. We show that one lane of paired-end RNA-Seq data can provide far more information about splicing than two lanes of single-end data, depending critically on properties of the distribution of cDNA fragment lengths in the sequenced library. MISO also leads to an intuitive method to detect diﬀerentially regulated exons or isoforms. Application of this method implicates the RNA splicing factor hnRNP H in regulation of alternative cleavage and polyadenylation, a role that is supported by UV crosslinking/immunoprecipitation/high-throughput sequencing (CLIP-Seq) analysis. Together, our results provide a probabilistic framework for RNA-Seq analysis, derive functional insights into pre-mRNA processing, and yield guidelines for the optimal design of RNA-Seq experiments for studies of gene and isoform expression.

2010-11-07 | GSE23694 | GEO

Alternative splicing regulation by homologous Muscleblind proteins

2016-06-01 | GSE79095 | GEO

Alternative splicing regulation by homologous Muscleblind proteins

Project description:We provide data showing alternative splicing regulation by Muscleblind proteins in MEFs. MEFs lacking functional Muscleblind (DKO MEFs) were stably reconstituted with Muscleblind proteins from Homo sapiens, Ciona intestinalis, Drosophila melanogaster, Caenorhabditis elegans or Trichoplax adhaerens and splicing regulation was explored using RNA-seq analysis followed by MISO (Mixture of Isoforms). Alternative splicing was accessed using RNA-sequencing data from five DKO MEF lines reconstituted with different GFP-tagged Muscleblind homologs or GFP alone and compared to RNA-seq data from three WT MEF lines and three control DKO MEFs (no Muscleblind reconstitution). A total of 12 samples were used for high-throughput sequencing.

2016-06-01 | E-GEOD-79095 | biostudies-arrayexpress

Ryu2017 - Generic human genome-scale metabolic model (Recon 2M.2)

Project description:Recon 2M.2 is a generic genome-scale metabolic model of Homo sapiens, in which a framework for gene-transcript-protein-reaction associations (GeTPRA) was deployed to generate metabolic reactions by considering the effects of alternative splicing of metabolic genes (i.e., both principal and non-principal transcripts). Eight versions of COBRA-compliant SBML files are available for Recon 2M.2 depending on the use of: MNXref versus BiGG IDs (metabolite IDs); Entrez gene IDs (GPR associations) versus Ensembl transcript IDs versus RefSeq transcript IDs versus UCSC transcript IDs (TPR associations for the last three database IDs).

2022-05-16 | MODEL2205110002 | BioModels

Identification of the O-GlcNAc-regulated alternative splicing events by performing RNA sequencing on HeLa cells with altered O-GlcNAc level.

Project description:We performed RNA sequencing on HeLa cells treated with OGT inhibitor (Ac4-5SGlcNAc), DMSO, or OGA inhibitor (Thiamet-G) and obtained about 100 million paired-end reads (150 bp) for each replicate. Then the sequencing data was analyzed by MISO to select the O-GlcNAc-regulated alternative splicing events.

2019-05-13 | GSE131067 | GEO

The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation, modulates translation and spliceosomal processes

Project description:The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation, modulates translation and spliceosomal processes

| PRJNA540514 | ENA

Comparison of splicing tools

Project description:Study that compares three commonly used event-based differential splicing tools: rMATS, MISO, and SUPPA2

2021-04-01 | GSE161144 | GEO