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).
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Illumina NextSeq2000 – Second generation sequencer with multi-laser sequencer (449nm, 523nm, 820nm). The flexibility of the platform allows to execute “Single read” sequences with reads of at least 50 nt and “Paired-End” with reads from 50 to 300 nt in length, with the possibility of setting at the beginning the exact length of the sequences that will be generated. The instrument offers high scalability with a wide choice of different flow-cell types capable of sequencing from a minimum of 100 million to a maximum of 1.8 billion molecules simultaneously, in a maximum of 48 hours and with an accuracy of ≥90%. Productivity from a minimum of 10 Gb to a maximum of 540 Gb of data per single run;
- 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.
- 10x Genomics ChromiumX – The 10x Genomics technology, a world leader for single-cell analysis, allows to separate from a few hundred up to 1 million cells isolated from both fresh samples and samples fixed in paraformaldehyde, preserving their biological state in the physiological conditions of collection. Thanks to its flexibility, ChromiumX allows to analyze up to 8 runs in parallel in standard throughput solutions and up to 16 runs in parallel during high throughput analyses. The instrument also allows multiplexing of different samples, up to a maximum of 12 in the same running channel (max. 96 samples for standard throughput analysis, max. 192 samples for high throughput analysis), drastically reducing not only the processing and analysis times, but also the cost per sample.
- Nanostring (Bruker) CosMx SMI – Spatial Multiomics Single-cell Platform – CosMx is a platform that integrates high-resolution imaging and cloud data analysis through the AtoMx™ integrated computing solution for single-cell spatial biology analyses. The technology is based on cyclic FISH (fluorescence in situ hybridization) hybridization chemistry capable of generating a unique optical code for each target ensuring high specificity and sensitivity. The flexibility of the instrument allows to analyze sections from formalin-fixed, paraffin-embedded (FFPE), fresh-frozen (FF), and fixed cell lines. Finally, CosMx allows to extremely sensitively define the expression of over 6000 RNA targets and 64 protein targets, at cellular and subcellular level with a resolution reaching 50 nm.
- 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.
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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.
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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.
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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)