Alternative splicing in adult human heart and brain
Ontology highlight
ABSTRACT: 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.
Project description: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.
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.
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.
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.
Project description:CELF4 regulates translation and local abundance of a vast set of mRNAs, including those that control homeostasis in excitatory neurons
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.
Project description:The heat-shock stress response was studied at the level of exons using Affymetrix Exon-array profiling for both sense and anti-sense transcripts. Sense transcript profiling was done as per the protocol of Affymetrix Exon 1.0 ST array and anti-sense transcript array profiling was done using a modified protocol (Xijin Ge et al., BMC Genomics. 2008 Jan 22;9:27). In short, for profiling antisense transcripts, first cycle cDNA synthesis and IVT step is skipped. This modified protocol starts directly from the second cycle cDNA synthesis step. The labelled target DNA fragments are in reverse orientation of original mRNAs. Thus the hybridization signals will represent transcripts from the same exonic regions but from the opposite DNA strand. Study was undertaken with 2 biological replicates each for - a) Heat-shock treated Sense b) Heat-shock treated Anti-sense c) Untreated control Sense d) Untreated control Anti-Sense
Project description:poly(A)+ RNA samples from hnRNP C siRNA knockdown and control HeLa cells were compared on a splice-junction microarray to detect changes in alternative splicing. Using the ASPIRE3 algorithm, we detected changes in splicing at 1,340 alternative exons. We observed a similar incidence of increased or decreased exon inclusion in hnRNP C knockdown cells, indicating that hnRNP C can either silence or enhance exon inclusion, respectively. We validated changes at 26 exons by RT-PCR with a 92% success rate.
Project description:The aim of our study is to increase understanding of the antiproliferative and pro-apoptotic potency of resveratrol by identifying genes which underlie involved pathological pathways and biological process. Therefore, we performed a gene Chip Transcription Analysis with subsequent Protein ANalysis THrough Evolutionary Relationships (PANTHER) analysis to evaluate which transcripted genes are significantly influenced by resveratrol. To determine the transcriptional profile of resveratrol, three biological replicates were processed on Affymetrix Gene Chip Human 1.0 ST.
Project description:Eptstein-Barr Virus, an oncogenic herpesvirus, infects and immortalizes human B cells in culture into indefinitely-prolerifating LCLs. We examined the gene expression of primary B cells during the process of infection and growth transformation at the exon level to analyze virus-induced changes in expression and exon usage. 4 samples each of total RNA were extracted from purified resting B Cells and monoclonal LCLs, for a total of 8. These samples were subjected to either Human Exon Array 1.0 or Affymetrix U133 2.0 plus. Data was then RMA normalized and analyzed using SplicerEx