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.
  • 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.
  • BD Rhapsody Single-Cell Analysis system (Express): The system enables high-throughput single-cell RNA-Seq analyses starting from single-cell suspensions. It uses a novel planar array of microwells for cell capture and a bead-based 3’ RNAseq assay. By conjugating a polyadenylated DNA barcode to a universal antibody, it is possible to multiplex up to 12 samples in one, to reduce experimental cost. Finally, BD AbSeq allows also simultaneous measurement of protein and RNA expression at the single-cell level.

  • Fragment Analyzer system: a multiplexed capillary electrophoresis (CE) instrument for performing automated, high throughput separation and quantification of nucleic acids (DNA and/or RNA). Separation is achieved by applying an electric field through a narrow bore (50μm) fused silica capillary array filled with various conductive gel matrices designed to sieve DNA/RNA molecules of a specific size range. The tool provides the DQN (DIN) or RQN (RIN) values of DNA or RNA integrity respectively.

  • The QuantStudio3 Real-Time PCR System: fluorescent-based polymerase chain reaction (PCR) instrument to perform Quantitative detection of target nucleic acid sequences (targets), Qualitative detection of targets (endpoint analysis) and Qualitative analysis of the PCR product (post-PCR melt curve analysis). The QuantStudio3 Systems is equipped with 0,2ml 96-well plate block and uses a coupled four-color filter set (4 excitation filters (450-600nm) e 4 emission filters (500-640nm)) that supports the FAM, VIC, ROX, SYBR, ABY, JUN and MUSTANG PURPLE dyes.

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

For each sample please compile the following form: Sample order sheet

For the 10x single cell analysis please use this form: 10x single cell sample order sheet

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