LAGE
The Genomics and Epigenomics Laboratory (LAGE) works on analysing DNA and RNA sequences and genotyping (microarrays). Based on an open-access model, the laboratory organises, integrates and optimises resources, expertise and experience in a single unit. It is a leading national centre in the field of genomics and epigenomics and promotes synergies between regional, national and international players.
The laboratory has 20 workstations equipped with the tools necessary for the preparation and management of samples during processing and interpretation of sequences. Researchers and technologists at LAGE are also involved in numerous collaborative scientific projects for standard and applied research. The laboratory also offers specially tailored services and consulting. The laboratory has been an Illumina Propel-Certified Service Provider for Infinium genotyping since 2018, and for the MiSeqDX instrument since 2020.
The Genomics and Epigenomics Laboratory is part of the Life Sciences Open Lab, an open research infrastructure in which core facilities and expertise create specialized functions capable of providing know-how and services aimed at carrying out experimental tests and applied and industrial research projects.
Studies and services for data sequencing and analysis
- Human, animal and microbial genome and transcriptome sequencing and analysis (DNA-seq and RNA-seq);
- Human exome sequencing and analysis;
- Gene panel sequencing analysis;
- Microbiome sequencing and analysis through taxonomic marker sequencing (16S/ITS), metagenomics and amplicon sequencing;
- Metagenomic sequencing in matrices of various types (food, soil etc.) through taxonomic marker sequencing (16S/ITS) and amplicon sequencing;
- MiRNA-seq and small RNA-seq sequencing for post-transcriptional gene regulation analysis, ChIP-seq to analyse DNA and histone protein interactions;
- Genotyping with microarrays;
- Methylation with microarrays;
- Individual sequence analysis.
Sequencing tools
A flexible, ultra-high throughput DNA sequencing system capable of sequencing up to 48 human genomes at a 30-fold depth in a single instrument run.
The instrument offers multiple flow cell formats, various read length configurations and the ability to analyse one or two flow cells at the same time to obtain data output ranging from approximately 160 Gb to 6 Tb and up to 20 billion reads per run, providing flexibility across a wide range of study applications and sizes.
An innovative array scanner that provides fast, sensitive and accurate imaging of Illumina BeadChips.
The iScan system is part of Illumina’s comprehensive portfolio of innovative assays for genotyping, copy number variation (CNV) analysis and DNA methylation. The scanners and components are modular, creating a system that can be synchronised and configured in accordance with varying levels of required sample throughput. The iScan system uses high performance lasers, optics and sensing systems to provide submicron resolution and high throughput. As a result, scan times are extremely fast while preserving data quality and reproducibility.
A massive parallel sequencing platform to be used both in certified IVD (In Vitro Diagnostic) and RUO (Research Use Only) analysis.
Illumina’s MiSeqDX System connects Illumina’s sequencing by synthesis (SBS) technology with a workflow that enables researchers to obtain analysed data from DNA samples in as little as eight hours (8h), producing up to 15 gigabases of data in a single instrument run, 25 million reads with a length of 2×300 bp each and base call accuracy parameters greater than 99.9%. MiSeq incorporates cluster generation, sequencing and data analysis functions on a single instrument with full automation and flexibility to process limited numbers of samples.
PromethION 24 offers direct, real-time DNA and RNA sequencing technology capable of long readings of single molecules.
The PromethION 24 system is designed to run 24 flow cells, allowing for on-demand sequencing, using any flow cell at any time. The running of single experiments can be started and stopped as required or multiple flow cells can be deployed onto single experiments for greater speed or throughput. Each flow cell allows up to 3,000 nanopores to be sequenced simultaneously, with a yield of > 4.8 Tb.
Laboratory equipment
The laboratory extends over an area of 220 square metres, housing 20 workstations on workbenches, one fume hood workstation and one horizontal laminar flow hood workstation. The workstations are set up with the following ancillary equipment used to prepare and handle samples during preliminary and preparatory processing for sequencing:
- Semi-automated TECAN EVO apparatus for parallel processing of 384 samples for the Infinium protocol (Tecan)
- Illumina Hybridization Oven (Illumina)
- Bioanalyzer (Agilent Technologies)
- PCR STEP One PLUS (Applied Biosystem)
- NanoDrop (ThermoFisher Scientific)
- cBot Cluster Generation System (Illumina)
- Covaris M220 ultrasonicator (Covaris)
- Tape Station System 4200 (Agilent Technologies)
- Class II biological safety cabinet certified to EN12469
Discover all the articles and studies published by the researchers at Area Science Park
Brilliant and determined minds are always welcome in Area Science Park!
Become part of our team and work in a dynamic and collaborative environment, contributing to the scientific progress we are driving.