Campus of Medicine of the University of Salerno (Baronissi, SA)

NGS (short reads) Illumina Novaseq6000 Sequencers

The NovaSeq 6000 platforms leverage Illumina next-generation sequencing (NGS) technology, multiple flow cell types, two parallel workflows, and multiple read length combinations. Users can choose and combine four types of flow cells (SP, S1, S2 or S4), process one or two flow cells at a time, and choose between different read lengths (1 X 35 bp, 2 X 50 bp, 2 x 100bp, 2 x 150bp, 2 x 250bp). The NovaSeq 6000 enables scalable and effective throughput from 80 Gb and 800 million reads to 3 Tb and 10 billion reads of data in single flow cell mode. In dual flow cell mode, the output can reach 6Tb and 20 billion reads. The system allows you to sequence up to 48 genomes in 48 hours with comprehensive coverage. The NovaSeq 6000 is compatible with a variety of library prep kits and supports a broad range of methods, such as expression profiling (RNA-seq), WES and WGS, metagenomics and metatranscriptomics analysis, single-cell sequencing, epigenome, and more.

NGS (short reads) Illumina Miseq Sequencer

The MiSeq System leverages Illumina's Sequencing by Synthesis (SBS) chemistry, a proven next-generation sequencing (NGS) technology.

The instrument offers the ability to adjust the length of the read, the option to use different types of flow cells, and the choice of unidirectional or paired-end reads (1 x 35 bp, 2 x 25 bp, 2 x 75 bp, 2 x 150 bp, 2 x 250 bp, 2 x 300 bp) providing the flexibility to tailor the data output to a wide range of experimental needs.

It is capable of automated paired-end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read.

The system is optimized for a variety of applications, such us targeted resequencing, small genomic and amplicon sequencing, 16S metagenomics, and more.

NGS (short reads) ThermoFisher Scientific Ion Torrent Genexus Sequencer

The Ion Torrent Genexus Integrated Sequencer is a next generation sequencing solution that enables an integrated workflow from sample quantitation to the final report with results delivered in one day only. Genexus Integrated Sequencer is designed for clinical oncology, microbial and infectious disease research as well as hereditary diseases, by enabling library preparation, sequencing and analysis in one instrument with a simple workflow, easy to set up and use. It integrates reporting capabilities without the need for an additional server with the possibility to process simultaneously several protocols in a single sequencing run.

NGS (long reads) Oxford Nanopore GridION Sequencer

Nanopore technology represents an efficient and highly scalable approach for the sequencing of nucleic acid fragments of variable length (from "short" to "ultra-long"), thus being a breakthrough in the assembly of genomes, direct nucleic acid sequencing and metagenomic analyses. The GridION platform is highly flexible, allowing to generate up to 250 Gb of data with a simple and linear workflow. By using Nanopore technology, it is possible, among others, to identify epigenetic modifications starting from native DNA and RNA molecules, fusion transcripts and gene isoforms, haplotypes and structural variants.

Liquid Handling System Hamilton Microlab MagEx STARlet

The Microlab MagEx STARlet workstation uses air displacement pipetting to achieve high measurement accuracy. Its pipetting technology achieves high accuracy, precision, and repeatability from sub-microliter to large volumes. DNA and RNA purification protocols have already been optimized on the workstation for up to 96 samples simultaneously starting from different biological matrices (blood, saliva, urine, tissues, soil, environmental samples, etc.), and can be used for downstream NGS applications. On the instrument, it is also possible to develop custom protocols according to the experimental needs of the users.

Liquid Handling Systems Hamilton Microlab NGS STAR

NGS STAR workstations are a complete solution for next-generation sequencing (NGS) applications that enable the preparation of a wide range of libraries, from whole genome to whole transcriptome sequencing and targeted resequencing applications. The NGS Star includes integrated components for pipetting, thermal incubation, shaking, PCR, and magnetic bead separation. This system enables fully automated library preparation, with a capacity of up to 96 sample libraries processed simultaneously, increasing uniformity and reproducibility at medium and high throughputs.

Single cell sequencing platform Takara Icell8 cx

The ICELL8 cx system is a single-cell analysis platform that combines the power of imaging and dispensing single cells in 5,184 nanowell chips. The ICELL8 cx system uses a single-cell isolation system without cell size bias and can process up to 8 samples simultaneously. The system allows the flexibility to analyze multiple parameters per experiment and uses the power of imaging to distinguish true single cells from multiple cells or empty wells, and live from dead cells.

This system is already validated for use with several NGS applications, such as complete transcriptome analysis, human TCR profiling and 5′ differential expression, 3′ differential expression, and genome mapping via ATAC-seq, but it also offers the flexibility to develop custom protocols.

Single cell sequencing platform 10x Genomics Single Cell Chromium Controller

The Chromium instrument uses advanced microfluidics to partition and barcode individual cells in minutes. Based on Gel Beads-in-Emulsion (GEM) technology, the Chromium Controller enables digital analysis of 3′ gene expressions, profiling 500-10,000 individual cells per sample. A pool of ~3,500,000 barcodes is used to index the transcriptome of each cell, and thousands of cells are processed simultaneously using a nanoliter-scale reaction volume. The controller enables single-cell analysis of CNV, gene expression, immune profiling, and ATAC.

Quantitative Nucleic Acid and Protein Analysis Platform NanoString nCounter SPRINT Profiler

The nCounter system uses a digital detection method capable of performing direct profiling of single molecules in a single reaction without the need for enzymatic reactions and with a very high degree of multiplexing. The system works by marking individual target nucleic acid molecules with a unique barcode consisting of a color code of fluorescent molecules.

The Platform can carry out the study of 800 targets simultaneously per sample, for analysis of gene expression (mRNA and miRNA) and copy Number Variation (DNA) in a completely automatic way and without the need for signal amplification or PCR step. This allows for avoiding the drawbacks normally deriving from the use of enzymatic systems, such as the introduction of bias and errors in the sequences of interest. The system allows work on material extracted even from highly degraded samples such as tissue fixed in formalin and embedded in paraffin (FFPE).

Spatial Transcriptomics System Nanostring GeoMx Digital Spatial Profiler

The GeoMx Digital Spatial Profiler (DSP) system combines spatial and molecular profiling technologies by generating a tissue image with single-cell resolution and digital data of the entire transcriptome or protein expression. This technology, which combines high-plex and high-throughput data, enables simultaneous in situ spatial analysis of proteins or mRNAs from a single tissue section, allowing the researcher to quickly and quantitatively assess the biological implications of heterogeneity in tissue samples, and locate, select, and analyze regions of interest (ROIs) from each sample. Expression levels of individual ROIs are then read using Illumina sequencers or the nCounter® SPRINT system.

Tapestri single cell DNA sequencing platform – Mission Bio

The Tapestri platform is the first system designed for simultaneous analysis of DNA and proteins across thousands of single cells. It is based on the principle of inclusion of isolated cells in drops of emulsion (droplets) which, following the addition of a unique barcode, represent the input for downstream analyzes for characterization of individual cells and rare populations, passing from single genotype typing to more complex genotype-phenotype association analyzes, specific to different cell sub-populations. The multi-omics approach allows parallel analysis of DNA and surface proteins on thousands of single cells, through the simultaneous detection of SNVs, CNVs and proteins.

Platform for circulating tumor cells genomic analyses - Menarini Silicon Biosystems DEPArray PLUS

It is an automated platform, which applies immunofluorescence and di-electrophoresis to identify and isolate rare cells with absolute purity degree (100%) from blood samples or, alternatively, from formalin fixed and paraffin embedded (FFPE) tissues.

It holds 9 fluorescence channels and high resolution for accurate identification from a minimum volume of input sample. Isolated cells can be used for downstream genetic investigations, including low-pass genome sequencing, CNV identification and cancer panels analysis.

Fluorescence microscope Leica THUNDER Imager 3D Tissue

The THUNDER imaging system uses opto-digital technology and the new Computational Clearing method to create high-resolution, high-contrast images. This technology allows you efficiently differentiates and eliminates background from wanted signal. The high sensitivity of the system guarantees a low level of phototoxicity and photobleaching. The THUNDER Imager 3D Tissue system is designed for real-time 3D fluorescent imaging of thick tissue sections, allows a clear view of details, even deep within an intact specimen, without blurring and is particularly indicated in studies of spatial transcriptomics.

Tecan Spark multi-mode microplate reader

Highly versatile system for spectrophotometric, fluorometric and luminescence microplate assays. The presence of a high-speed monochromator makes it particularly suitable for rapid and accurate absorbance measurements; the "NanoQuant Plate" device enables microvolumetric nucleic acid analyses for qualitative and quantitative evaluations, allowing to analyze up to 16 samples simultaneously in a volume of 2 µl. This makes Spark particularly suitable for high throughput sample quantization and quality controls . In addition to absorbance measurements, the NanoQuant plate can be used for fluorescence signals detection on microvolume samples from multiple assays. The combination of filters and monochromator allows to reach a high sensitivity of fluorescence detection. Finally, the presence of a cell imaging module integrated into the reader, allows automatic cell counting, as well as cell viability assays, bright field imaging and automated assessment of cell confluence on microplates.

SONY MA900 Cell Sorter flow cytometer

The MA900 system operates through micro-fluidics chips, comprehensive fluidic controls, and advanced automation that greatly simplify cell separation procedures making them less subjective thus improving reliability. The MA900 offers a wide flexibility, allowing the detection of up to 14 parameters thanks to 4 excitation lasers (488 nm, 405 nm, 561 nm and 638 nm). With the highest level of automation available compared to any flow cytometer separator, the MA900 utilizes sensors, software and engineering know-how throughout a workflow enabling separation down to a single cell resulting ideal for downstream single cell/single nucleus sequencing applications.

Platform for cell and nuclei purification LevitasBio LeviCell 1.0 System

The LeviCell system allows cell separation, based on a magnetic field, without stress for the cells themselves, keeping them intact and vital. The system is capable of processing a broad spectrum of sample types, from primary dissociated tissue to various types of fragile or easily stimulated cells. Purified cells of interest are reliably recovered regardless of starting cell number, cell viability, or sample purity.

DELL HPC High Capacity Computing Center and Data Storage

The DELL computing infrastructure (HPC) is one of the main technological tools available within the center, capable of storing, processing data and performing complex calculations at high speed. The computing system is equipped with 1200 CPU cores, 8 Nvidia RTX a100 GPUs, 10Tb of RAM and a 3 Pb Dell EMC Isilon data storage, in the process of GDPR certification. The computer center is connected to the GARR network, which connects the education and research communities via ultra-broadband. The CRGS is also a partner of ELIXIR, the European Research Technology Infrastructure for Biological and Bioinformatics Data.

Translated with Linguana