Sequencing and Analysis

We peer into the genomic landscapes of humans, animals, plants, microbes and viruses through DNA-seq and RNA-seq techniques, unravelling the genetic blueprints that underpin biological mechanisms, physiological responses to exogenous stimuli, diseases and their susceptibility and progression.

DNA Sequencing

The facility offers whole genome sequencing (WGS), an effective tool for both de novo and re-sequencing. De novo sequencing generates the first map for a given species genome, thus providing a valuable reference for targeted or re-sequencing (such as exome-seq or based on the enrichment of specific regions due to hybridization capture). Such protocols can be performed both on Illumina and ONT platform, giving the chance to explore the long reads. Furthermore, WGS could be useful for identification of Single Nucleotide Polymorphisms (SNPs), insertions and deletions (Indels), Structure Variations (SVs) and Copy Number Variations (CNV), that all together can give rise to Genome Wide Associate Studies (GWAS) and correlate such variations to specific phenotype.
In addition to this, our personnel has extensive experience in DNA methylation, a secondary modification on non-coding genes loci that prevents the binds of DNA interacting factors. Several techniques, including reduced representation bisulfite sequencing (RRBS) and Infinium CytoSNP-850K BeadChip, preserve DNA methylation and simultaneously transform it into quantitative and measurable signals that provide essential information on biological phenomena. Illumina DNA microarray technology (also known as BeadArray technology) uses silica microbeads, on which surface hundreds of thousands to millions of genotypes for a single individual can be assayed at once. We use such technique for genotyping and for the detection of methylation, allowing highly accurate and precise quantification of methylation levels in the genome at the level of single CpG sites.
Furthermore, the mechanism of protein-DNA interaction, also strongly affected by methylation, is crucial for understanding cellular processes, for both endo and exogenous (viral) transcription factors.

RNA Sequencing

Regarding RNA, we have a strong background on RNA-sequencing, including mRNA, and noncoding RNA. Altogether, these RNAs compose the transcriptome, that allows the quantification of the relative abundance of transcripts, the identification of alternative splicing isoforms, and post-transcriptional RNA editing events. Alongside the RNA messengers, we are able to implement the analyses with the characterization of small, long non-coding, miRNA-seq, that provide direct insight into host–pathogen interplay.

Microbiome Profiling

Delve into the microbial world with microbiome sequencing and analysis, through taxonomic marker sequencing (16S/ITS), metagenomics, and amplicon sequencing. Explore the intricate ecosystems within various matrices, from soil to foodstuffs, unravelling the microbial diversity crucial for ecological balance and human health.