NGS

Short- and long-read nucleic acids sequencing

In the Genomics Core Facility are available short- and long-reads NGS technologies to sequence nucleic acids from different biological matrixes and sources.

Short-read sequencing platforms available include Illumina (NovaSeq6000, MiSeq and MiSeq Dx, NextSeq 550 Sequencing System) and Thermo Fisher (Genexus)while long-read platform Oxford Nanopore Technologies (GridION), produces longer sequences with higher accuracy. All the sequencers are supported by automated systems for high throughput library preparation from Hamilton (MagEx and NGS STAR).

Single cell sequencing and Spatial transcriptomics

The Single Cell Profiling core facility comprises up-to-date technologies to perform genomic analyses at single cell level, for in depth understanding of biological and genetic cellular functions. In the Single Cell Sequencing Laboratory (scSeq), are available technological platforms for studies of single cell genomics (DNA, RNA and epigenome) and spatial transcriptomics from 10X Genomics (Chromium), SMARTer ICELL8 cx Single Cell from Takara (SMARTer ICELL8 cx Single Cell), MissionBio (Tapestry) and Nanostring (nCounter Analysis System and GeoMx Digital Spatial Profiler). The laboratory comprises also technologies for cell separation and sorting, including a  Sony MA900 sorter based on micro-fluidic chips and advanced automation that simplifies cell sorting and a BD FACSMelody flow cytometer, a LevitasBIO system from LeviCell, capable of separating a broad spectrum of cell types thanks based upon  the properties of their magnetic field, and a DEPArray from Menarini Silicon Biosystems, allows to identify, separate and analyse by NGS cells using high-resolution fluorescence and bright field images, useful also for  isolation and characterization of circulating tumor cells.

Gene editing-based genome-wide screenings

The Gene Editing facility applies gene editing technologies, such as CRISPR/Cas, to study the function of genes also at a genome-wide level. The CRGS offers the possibility of verifying the efficiency of gene editing downstream of CRISPR-Cas9-mediated gene silencing procedures. For this purpose, next generation sequencing of amplicons derived from the modified cell population or Sanger sequencing of amplicons cloned into plasmids can provide an accurate evaluation of the editing rate as well as a specific assessment of the inserted modifications.

BIOINFORMATICS AND HIGH PERFORMANCE COMPUTING

Each CRGS hub has its own Computing Infrastructure (HPC) dedicated to bioinformatics and eHealth capable of processing and storing large volumes of data and performing complex computations at high speed.