The Genomics Facility (GEFA) provides access to a wide range of cutting-edge techniques for genomic, transcriptomic, epigenomic and single cell analysis. Its aim is to enable the IIT scientists to get their own genomic experiments entirely performed, from the experiment set-up until data delivery and interpretation.
The GEFA operates along the entire data generation process, including but not limited to 1) starting material QC, 2) libraries preparation, 3) QC-passed sequencing data generation and release, 4) internal Laboratory Information Management System (LIMS) management. The starting material is mainly DNA/RNA derived from any sources and species (animal, plant, prokaryotic, etc.).
There are some “standardized” protocols, which are definitively and robustly running on the automatization and the data are released within a well-defined due-date. They now include: Total RNAseq, PoliA+ RNAseq, shotgun and PCR-free Whole Genome Sequencing, Whole Exome Sequencing and Metagenomics. Moreover, the Genomics Facility supports the scientists also with “non-standard” protocols set-up, with priority level depending on resources availability.
The GEFA operates both on “short reads” (SRS) (© Illumina) and “long reads” (LRS) (©Oxford Nanopore Technologies) sequencing technologies.
Below a non-exhaustive but representative list of the possible fields of application of the above-mentioned methods:
- RNA Sequencing (RNAseq) analysis: which includes Total RNA, PoliA+ RNA, small RNA
- Viral/bacterial Genome sequencing
- Single Cell Trascriptomics
- DNA Sequencing (DNAseq) analysis, which includes “Whole genome sequencing” (WGS), whole exome sequencing (WES), targeted sequencing, chromatin immunoprecipitation sequencing (ChipSEQ), HiSeq, metagenomics, epigenomic analysis.
The GEFA it is equipped with state-of-art instrumentation such as:
- NovaSeq™ 6000 System (Illumina), a short-read DNA sequencer able to produce up to 6 Terabases/run
- PromethION 24 (Oxford Nanopore Technologies) intended for long DNA/RNA reads sequencing
- Chromium Genome (10X Genomics), a system enabling the single cell transcriptomic profiling, starting from hundreds to millions of cells
- 5200 Fragment Analyzer System (Agilent Technologies), an automated parallel capillary electrophoresis system
- Microlab STAR Liquid Handling System (Hamilton), a fully automatized liquid handler intended for the NGS library preparation. It is equipped with 8 pipetting channels plus a 96-channel head
- SH800S cell sorter (Sony Biotechnology), sorting of a wide range of cell sizes for many applications using the 70-μm, 100-μm, and 130-μm microfluidic sorting chips