Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
Project description:One important obstacle in using softwood in biorefineries is its recalcitrance to enzymatic saccharification. In the present work, Thermothielavioides terrestris LPH172 was cultivated on three different steam-pretreated spruce materials and on non-treated spruce, harboring different hemicellulose content and structural characteristics. The aim of the work was to map the substrate-induced changes in the secretome of T. terrestris when grown on differently treated spruce materials and evaluate the hydrolytic efficiency of the secretome as supplement of a commercial enzyme mixture. The cultivation of T. terrestris was monitored by enzyme activity measurements of endo-cellulase, endo-xylanase, endo-mannanase, laccase and peroxidase. Proteomic analysis was performed on the secretomes induced by these materials to map the differences in enzyme expression.