Transcriptomics analysis of SARS-CoV2-induced changes in human lung epithelial Calu-3 cells
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ABSTRACT: RNA-Seq was carried out in order to obtain the time dependent expression dynamics of SARS-CoV2 (Trondheim strain)-induced transcriptome changes in human lung epithelial Calu-3 cells.
Project description:RNA-Seq was carried out in order to obtain the expression profile of lipopolysaccharide (LPS)-induced transcriptome changes in PMA-differentiated human THP-1 cell line.
Project description:Eliminating B cells through anti-CD20 antibody led to a drastic reshaping of the inflammatory tumor microenvironment. This included a profound reduction of T cells, endothelial cells, monocytes and fibroblasts. The results of this study are therefore the first evidence in human that B cells are required to sustain the inflammatory tumor microenvironment.
Project description:This experiment showed a distinct phenotypic and functional change in B cells induced by melanoma conditioned medium. Therefore, B cells are directly activated by melanoma cells. It furthermore shows, that B cells express a wide variety of genes that indicate that B cells have a strong effect on the composition of the whole tumor microenvironment.
Project description:The objective of this study was to decipher the metabolism expressed by Lactobacillus delbrueckii subsp. delbrueckii CIRM-BIA865 during soy juice fermentation using transcriptomics. The whole genome was sequenced, assembled and annotated. CIRM-BIA865 was then used to ferment soy juice to produce a soy-based yogurt. Samples were analysed in kinetics during fermentation, at pH values of 6.5, 6, 5 and 4.6. RNA from CIRM-BIA865 were extracted and sequenced using paired-end Illumina. Reads were mapped using Bowtie2 on previously obtained genome of CIRM-BIA865. No mismatch were allowed. Reads mapped on CDS were counted using htseqcount.List of differentially expressed (DE) genes between two successive sampling times (determined by pH) were generated using DEseq2 with a modified t-test and a p-value adjusted by Bonferoni inferior to 0.05. Fold changes expressed how many times genes were induced along the fermentations.
Project description:In this study monoclonal cell lines carrying mutations in the small nucleolar RNA host-gene GAS5 were obtained. Next, Poly(A) RNA-seq and Small RNA-seq analyses of obtained cell lines were performed on an Illumina NextSeq 500 platform. Poly(A) RNA-seq libraries was constructed on polyA mRNA-enriched fraction. Small RNA-seq libraries was constructed on small RNA fraction (<200 nucleotide length). The reads were aligned via STAR to the human genome (GRCh37). The comparison of the mRNA levels of genes and small RNA levels in RNA-Seq experiments was carried out using CuffDiff tool. Sashimi plots for RNA-Seq analyses of isoform expression were generated by IGV. It was shown that specific mutations in SNORD74 led to the downregulation of all GAS5-encoded SNORDs and GAS5 lncRNA. Obtained results demonstrate the SNORD-dependent manner of the GAS5 maturation.
Project description:poly-A enrichment RNASeq on RNA samples isolated from SupT1 cells with lentiviral mediated CRISPR SOX4 and HOXD3 KO against wildtype SupT1 during the time course of HIV infection (uninfected, 8, 18, 30 and 42hpi). SupT1 cells were spinofected with NLENG1-IRES G1I molecular HIV-1 clone. After RNA isolation, libraries were prepared with Ilumina TruSeq Stranded mRNA LT-Kit and sequenced on a llumina HiSeq 3000/4000 instrument.
Project description:To study expression pattern of small nucleolar RNAs (snoRNAs) during influenza A viral infection, human cells A549 were infected with influenza A/Puerto Rico/8/1934 (H1N1) virus. Small RNA-seq analysis of infected cells after 24 h or 48 h incubation was performed on an Illumina NextSeq 500 platform. The same mock-infected cells were used as control. Small RNA fractions (<200 nucleotide length) was used for constructing of cDNA libraries. Differential expressed non-coding RNAs were identified using R package DESeq2.
Project description:Blood samples from patients with myeloid malignancies were analyzed using whole exome sequencing (WES). Data set from genotyping by microarray of the same samples has been deposited in ArrayExpress under accession number E-MTAB-1845 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1845/).
Project description:We generated longitudinal genome-wide whole-blood miRNA profiles for the four multiple autoantibody-positive cases and their sex, age, and HLA-risk matched controls (a total of 87 samples), using the miRNA-sequencing approach.
Project description:Coq9R239X mice, a model of mitochondrial encephalopathy due to Coenzyme Q deficiency, were treated with Rapamycin administered in the chow at two different concentrations, i.e. 28 ppm and 225 ppm. The results are compared to those obtained in untreated Coq9R239X mice and untreated Coq9+/+ mice.