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: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: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: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: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:Lotus japonicus is a model legume broadly used to study transcriptome regulation under different stress conditions and microorganism interaction. Understanding how this model plant protects itself against pathogens will certainly help to develop more tolerant cultivars in economically important Lotus species as well as in other legumes. In order to uncover the most important defense mechanisms activated upon bacterial attack, we explored by microarray analysis the transcriptome regulation occurring in the phenotypically contrasting ecotypes MG-20 and Gifu B-129 of L. japonicus after inoculation with the non-pathogenic strain Pseudomonas syringae DC3000 pv. tomato.
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
Project description:Different inbred strains of rats differ in their susceptibility to OIR, an animal model of human retinopathy of prematurity. We examined gene expression profiles in Fischer 344 (F344, resistant to OIR) and Sprague Dawley (SD, susceptible to OIR) rats at the early time point of day 3 to identifying gene pathways related to the underlying genetic cause of phenotypic differences between strains. To examine gene expression changes in rats strains which are resistant and susceptible to OIR, four different experimental conditions were analysed: F344 cyclic hyperoxia (O2) exposed, F344 room air (RA) exposed, SD O2 exposed and SD RA exposed. A minimum of two samples of pooled RNA, comprising of 3 individual rats from 2 separate litters, was used for each experimental condition. Pooled RNA from different rats were used as biological replicates. An additional sample for F344 O2 and SD RA rats was included on the basis of the principal components analysis from the initial 8 samples. Pooled RNA from age-matched room air-exposed rats were used as controls.