Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sf3b1-dependent splice factor expression and alternative splicing in NMC

ABSTRACT: Neonatal mouse cardiomyocytes (NMC) were cultured in hypoxia (3% O2) with and without a lentiviral shRNA-mediated knockdown of Sf3b1. Total RNA was extracted from NMC using RNeasy kit, cDNA was synthesized using GeneChip WT cDNA Synthesis and Amplification kit (Affymetrix 900673) and hybridised to Affymetrix mouse high-resolution AltSplice microarrays.

ORGANISM(S): Mus musculus

SUBMITTER: Yann Christinat

PROVIDER: E-MTAB-3203 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Hif1-alpha dependent splice factor expression and alternative splicing in neonatal mouse cardiomyocytes (NMC)

Project description:Neonatal mouse cardiomyocytes (NMC) were cultured in normoxia (21% O2) or hypoxia (3% O2) with and without a lentiviral shRNA-mediated knockdown of Hif1-alpha. Total RNA was extracted from NMC using RNeasy kit, cDNA was synthesized using GeneChip WT cDNA Synthesis and Amplification kit (Affymetrix 900673) and hybridised to Affymetrix mouse high-resolution AltSplice microarrays.

2015-06-02 | E-MTAB-2652 | biostudies-arrayexpress

Alternative splicing in Mouse E18 brain

Project description:Total RNA was extracted from wild-type and FUS -/- mouse E18 brain samples using RNeasy kit, cDNA was synthesized using GeneChip WT cDNA Synthesis and Amplification kit (Affymetrix 900673) and hybridised to Affymetrix mouse high-resolution AltSplice microarrays.

2013-07-30 | E-MTAB-1229 | biostudies-arrayexpress

CELF4 microarray

Project description:CELF4 regulates translation and local abundance of a vast set of mRNAs, including those that control homeostasis in excitatory neurons

2012-12-12 | E-MTAB-1163 | biostudies-arrayexpress

Alternative splicing in adult human heart and brain

Project description:RNA was obtained from Biochain, cDNA was synthesized using GeneChip WT cDNA Synthesis and Amplification kit (Affymetrix 900673) and hybridised to Affymetrix human high-resolution AltSplice microarrays.

2014-01-22 | E-MTAB-1911 | biostudies-arrayexpress

Alternative splicing in human temporal cortex

Project description:We analysed changes in transcript levels and alternative splicing in the temporal cortex of individuals of different ages that were cognitively normal, affected by frontotemporal lobar degeneration (FTLD), or affected by Alzheimer's disease (AD). Our experiment's purpose is to provide new insights into the gene expression changes that distinguish healthy aging from neurodegeneration and identify the candidate regulators of alternative splicing that are associated with both processes.

2012-04-27 | E-MTAB-656 | biostudies-arrayexpress

Gene expression in hypoxic non-small cell lung cancer

Project description:Hypoxia triggers aggressive cancer growth and contributes to chemotherapy resistance. Novel therapeutic strategies aim at targeting hypoxia activated signaling pathways. Tumor hypoxia not only affects neoplastic tumor cells but also the surrounding stroma cells. Therefore, a novel ex vivo model was established, which allows the study of hypoxia effects in fragments of non-small cell lung cancer (NSCLC) with preserved tumor microenvironment and 3D-structure. Microarray analysis identified 107 significantly regulated genes with at least two-fold expression change in hypoxic compared to normoxic fragments. However, only four genes were significantly regulated in both subtypes, adenocarcinoma and squamous cell carcinoma. The hypoxic regulation of these four genes was verified in an independent set using quantitative PCR. Non-small cell lung cancer (NSCLC) fragments were cultured ex vivo under hypoxia or normoxia for three days. cDNA microarray analysis was performed in hypoxic and normoxic lung cancer fragments from ten patients.

2011-07-27 | E-GEOD-30979 | biostudies-arrayexpress

Bioinformatic analysis of membrane and associated proteins in murine cardiomyocytes and human myocardium

Project description:In the current study we examined several proteomic- and RNA-Seq-based datasets of cardiac-enriched, cell-surface and membrane-associated proteins in human fetal and mouse neonatal ventricular cardiomyocytes. By integrating available microarray and tissue expression profiles along with MGI phenotypic analysis, we identified 173 membrane-associated proteins that are cardiac-enriched, conserved amongst eukaryotic species, and have not yet been linked to a ‘cardiac’ Phenotype-Ontology. To highlight the utility of this dataset, we selected several proteins to investigate more carefully, including FAM162A, MCT1, and COX20, to show cardiac enrichment, subcellular distribution and expression patterns in disease. Three-dimensional imaging was used to validate subcellular localization and expression in adult mouse ventricular cardiomyocytes. FAM162A, MCT1, and COX20 were differentially expressed at the transcriptomic and proteomic levels in multiple models of mouse and human heart diseases and may represent potential diagnostic and therapeutic targets for human dilated and ischemic cardiomyopathies. Altogether, we believe this comprehensive cardiomyocyte membrane proteome dataset will prove instrumental to future investigations aimed at characterizing heart disease markers and/or therapeutic targets for heart failure.

2020-11-17 | PXD017732 | Pride

Neonat cardiomyocytes_hypertrophy_HDAC4

Project description:In order to identify targets for HDAC4, NRVM were infected with adenoviral vectors encoding beta-Galactosidase or Flag- HDAC4, and incubated in serum free or 10% fetal calf serum containing growth medium for 48 hrs. NRVM were infected with adenoviral vectors encoding beta-Galactosidase (control) or Flag- HDAC4 (experiment), and incubated in serum free or 10% fetal calf serum containing growth medium for 48 hrs. 2 biological samples of each condition were analyzed.

2011-01-01 | E-GEOD-19771 | biostudies-arrayexpress

Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte [expression array]

Project description:We compared Sox9-association at chondrocyte targets to a broad catalogue of regulatory indicators of chromatin organization and transcriptional activity to determine Sox9’s direct regulatory actions in normal developing chondrocytes. Sox9-associated regions resolve into two distinct regulatory categories. Class I regions closely associate with transcriptional start sites (TSSs). Their targets reflect general regulators of basal cell activities that Sox9 engages indirectly though a likely association with the basal transcriptional complex. In contrast, Class II regions outside of the local TSS domains highlight evolutionarily conserved, active enhancers directing expression of chondrocyte specific target genes, though DNA binding of Sox9-dimers at target sites with sub-optimal binding affinity. The level of associated chondrocyte gene expression correlates with the number of enhancer modules around the target gene and grouping into super-enhancer clusters. Comparison of Sox9 programs between neural crest and mesoderm-derived chondrocytes points to similar modes of chondrocyte specification in distinct chondrocyte lineages. These data provide the first insight into mammalian Sox family actions at the genome scale in the vivo setting. The resulting enhancer sets provide a key resource for further dissection of the regulatory programs of mammalian chondrogenesis. Incorportation of ChIP-seq data of Sox9 and histone modification marks for chromatin status together with microrarray gene expression profiling in neonatal mice chondrocytes to uncover Sox9 regulatory system

2015-07-01 | E-GEOD-69108 | biostudies-arrayexpress

The potential of remdesivir to affect function, metabolism and proliferation of in vitro heart and kidney models

Project description:Here, we performed an in vitro toxicity assessment for remdesivir at clinically relevant concentrations around the cmax of 9 µM using H9c2 rat cardiomyoblasts and neonatal mouse cardiomyocytes (NMCM) as heart models and rat NRK-52E cells and human RPTEC/TERT1 cells as kidney models. Due to the tendency of nucleoside analogs for mitochondrial toxicity, we focused on metabolic changes and mitochondrial function. Additionally, we analyzed the functionality of NMCM and determined early proteomic changes.

2022-05-24 | PXD029311 | Pride

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