Project description:We applied small RNA sequencing technology to identify precursor tRNA derived small RNA expression in human cancer cell lines and human liver tissues.
Project description:Small RNA-Seq study comparing Epstein-Barr virus (EBV) infected BJAB-B1 cells to isogenic, but uninfected, BJAB cells. The goal was to deduce differentially expressed small ncRNAs both micro and non-micro (up to 200 nt) between the two cell lines to gain insights into EBV-associated deregulation of host small ncRNAs.
Project description:We analyze whether tRNA quantifications based on small RNA-seq data are informative enough to distinguish between different human cell lines covering multiple tissue types. We therefore apply both small RNA-seq and Hydro-tRNAseq to HEK293 (kidney), HCT116 (colon), HeLa (cervix), MDA-MB-231 (breast), and BJ fibroblasts. First, the correlations between the two methods of identical samples and computational mapping pipeline range between 0.93 and 0.96 for all cell lines. tRNA quantifications from both protocols are compared and significantly higher Spearman correlations are obtained within matching samples versus mismatching cell lines. In consequence, we demonstrate that small RNA-seq quantifications of sample-specific tRNA profiles show a good agreement with conventional tRNA-seq.
Project description:Here, variants of 29 breast cancer cell lines were called on RNA-seq data via HaplotypeCaller. Low read depth sites (<5), RNA edit sites, and low complexity regions (LCRs) were excluded. Common variants were filtered using 1000 genomes, gnomAD, and dbSNP data. Starting from hundred thousands of single nucleotide variants (SNVs) and small insertions and deletions (InDels), a thousand variants remained after filtering for each sample.