Our institute disposes of a well-established NGS facility which offers assistance in pursuing state-of-the-art translational research projects involving next generation sequencing. The support starts with advice and guidance for the project followed by the NGS library preparation, quality control and sequencing. If requested, our computational biology team can take care of all subsequent analysis steps.
The facility has a more than 10 years of experience with various types of applications involving genomics, transcriptomics, epigenomics but also more recently single cell and spatial transcriptomic analysis.
Sequencing is performed on Illumina (NovaSeq 6000, NextSeq 500 and a MiSeq) or for long-read sequencing on ONT (MinION) instruments. For the single cell analysis in a low throughput manner, we can exploit the DEPArray, for high throughput the 10x Chromium Controller or the BD Rhapsody. The GeoMx DSP instrument available in our institute enables spatial transcriptomics to analyse the expression in its morphological context. For a smaller subset of RNA, DNA or protein targets we can also offer the nCounter platform. A Hamilton Microlab STAR liquid handling system permits an automated library preparation of up to 96 samples. The equipment includes also the Covaris M220 Focused-ultrasonicator for reproducible genomic DNA shearing or the 4200 TapeStation or 2100 Bioanalyzer for all quality control procedures.
Our portfolio of transcriptomic analysis includes long RNA but also small RNA, circRNA or m6A-RNA sequencing. The epigenomic approaches comprise ChIP-Seq, ATAC-Seq, HiC-Seq, DRIP-Seq, ChIRP-Seq, ChIRP-RNA-Seq and MeDIP-Seq to characterize the tumour phenotype beyond mutations.
Our facility is also involved in various projects promoted by the network Alleanza Contro il Cancro and participates in the COVID sequencing within the COROnet.