Project description:Caco-2 cells were infected with F. nucleatum (MOI=100:1) or non-infected (control) for 24 hours. Total RNA of cells was extracted using the TRIzol® Reagent (Life Technologies) and cDNA was generated using the PimeScript TMRT Reagent Kit (Takara). We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
Project description:Caco-2 cells grown on transwells were infected with Japanese encephalitis virus (JEV) and total RNA was isolated from cells at the time when trans-epithelial electrical resistance was reduced by about 50% of uninfected cells
Project description:Common missense mutations (D299G, T399I) have been recently identified in the human TLR4 gene. The aim of this study was to determine how TLR4 and associated mutants affect gene expression in Caco-2 cells. We used microarrays to asses gene expression profiles in Caco-2 stably overexpressing TLR4-WT, TLR4-D299G, TLR4-T399I or untransfected.
Project description:PURPOSE: We generated NAPE-PLD-deleted Caco-2 cells, which is a model of intestinal epithelial cells, using genome editing with the CRISPR/Cas9 system. To explore the molecular events following the deletion of NAPE-PLD in Caco-2 cells, we examined the transcriptomic changes in the NAPE-PLD deleted clone 35 compared with Caco-2 parent cells by RNA-seq. METHODS: mRNA profiles of parent and NAPE-PLD deleted Caco-2 cells were generated using Illumina HiSeq4000 (n=2/each cell). Those raw sequence data were then mapped to the human hg38 reference genome using a custom MOIRAI pipeline with STAR 2.51 for alignment. Then, read counts for each transcript were obtained using featureCounts, and the raw count data were directly analyzed for differential gene expression by using edgeR 3.20.9. RESULTS: Approximately 40 million reads per sample were obtained as raw data. Among a total of 12,331 genes detected in at least in one cell type, 1,019 genes were up-regulated (FDR < 0.01, logFC > 1) and 827 genes were down-regulated (FDR < 0.01, logFC > 1) in clone 35 compared with the parental cells.
Project description:Human astrovirus infection is known to disrupt intestinal barrier function by increasing barrier permeabilty. However, the exact cellular mechanism(s) involved is unknown. We used microarrays to detail the global gene expression changes occuring during astrovirus infection and identify necessary cellular pathways for astrovirus pathogenesis.
Project description:Common missense mutations (D299G, T399I) have been recently identified in the human TLR4 gene. The aim of this study was to determine how TLR4 and associated mutants affect gene expression in Caco-2 cells. We used microarrays to asses gene expression profiles in Caco-2 stably overexpressing TLR4-WT, TLR4-D299G, TLR4-T399I or untransfected. Caco-2 clones stably overexpressing HA-tagged wildtype TLR4-WT, mutant TLR4-D299G or TLR4-T399I were generated. Prior to analysis, cell clones were cultured for 8 days in all experiments. RNA (triplicate) was extracted and hybridized on Affymetrix microarrays.