Platforms

Genomics and transcriptomics platform

The platform deals, through the use of the latest technologies and tools available, to analyze the entire transcriptome and the genome of microorganisms, animal plants and naturally human. The services offered by the Genomics and transcriptomics platform include the preparation of libraries starting from DNA and RNA samples, genotyping using technologies based on PCR and sequencing using second generation technologies (Next Generation Sequencing).

  • Illumina NextSeq 500. Second generation sequencer equipped with 2 lasers (520nm and 650nm) and 2 emission filters for reading the nucleotide sequence. It allows to generate 150bp paired-end sequences in very short times. Each sequencing run requires a maximum of 29 hours and produces a total output of 120 billion bases, corresponding to 1 human genome (40X), 6-12 esomes or 16 transcriptomes.
  • Illumina MiSeqDX. Parallel massive sequencing platform to be used both in IVD (In Vitro Diagnostic) and RUO (Research Use Only). It allows to produce sequences up to 300 nucleotides (nt) in paired ends (2 x 300bp). Each sequencing run requires from 4 to 55 hours depending on the selected mode and can generates up to 25 Millions of fragments.
  • 10X Genomics Chromium System. Platform for the preparation of single cell libraries (possibility of capture up to 100-80000 individual cells in 10 minutes) and for the production of linked products reads in phase, for the characterization of haplotypes and the assembly de novo of the genomes. The microfluidic circuits rapidly partition input samples (e.g. high molecular weight DNA, single cells) which are then barcoded using GemCode™ technology. Chromium utilizes 8-channel chips enabling up to 8 samples per run (1 sample per channel). Downstream application-specific assays generate barcoded libraries for sequencing on Illumina sequencing systems. GemCode™ Gel-Beads deliver assay-specific oligonucleotides into nanoliter-scale liquid/oil emulsion partitions for barcoding and amplification of target nucleic acid templates.
  • ViiA7, 7900HT Fast Real-Time PCR System. Thermal cycler for simultaneous real-time PCR analysis of 384 different reactions in reaction volumes even of only 1μl, with ability to carry out reactions in fast mode (35 min for single plate versus 2 traditional hours) and with possibility of multiplexing up to four analyzes per well (for a total of 1536 analyzes per plate). The instrument, which can mount a 96-well block, is coupled to a plate set-up robot (EpiMotion and Eppendorf). This tool is outsourcing.
  • Illumina MiSeq FGx. Second generation sequencer equipped with 2 lasers (530nm, 660nm) capable of generating up to 50 million paired-end sequences per fragment with lengths up to 300bp. Each sequencing run takes 4 to 56 hours and produces a total output of 15 billion bases. It is used for the sequencing of gene panels for applications in the diagnosis of tumors and genetic-based diseases and in forensic medicine. This tool is outsourcing.
  • QX200 Droplet Digital PCR system Biorad Biorad. System for digital PCR based on water-oil emulsion nanoliter-sized droplets technology. Using the QX200 Droplet Generator a sample is subdivided in 20000 droplets and, inside of each droplet, the PCR reaction is performed in a similar manner as real-time PCR that use Taqman idrolisis probes or intercalating dye as EvaGreen. After the PCR, inside the QX200 Droplet Reader, the fraction of fluorescent positive droplets is determined and, using the Piosson statistics, the target DNA concentration in original sample is calculated. This technology allows a lot of applications, for example absolute quantification, copy number variation, gene expression and miRNA analysis.
  • ddSeq single cell isolator (Bio-rad). Instrument for single cell gene expression that works with “Illumina® Bio-Rad® SureCell™ WTA 3′ Library Prep Kit. The istrument, using a microfluidic technology, coencapsulates single cells and barcodes in subnanoliter droplets where cell lysis and barcoding are performed. Afterwards RNA-seq libraries are prepared and sequenced.

For info and booking, see the Access and Booking page.

Platform Managers: Monica Castellucci e Francesca Griggio (045 8027220)

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