The platform offers a catalog of services tailored to the specific needs of each experimental design. We operate under a competitive public pricing model for public research centers, universities, and private entities (see current rates in the Pricing section).

Consulting services

Methodological advice in experimental design, preparation of budgets for funding applications in research projects, and support in training activities.

Automated experimental laboratory services

Advanced analytical quality control and sample processing. Automated integrity assays to ensure project viability:

• Automated capillary electrophoresis (Bioanalyzer) for RNA and DNA quality control.
• Specific quality control by Illumina qPCR for critical paraffin-embedded samples (FFPE).
• High-sensitivity fluorometric quantification in plates and individual tubes (PicoGreen and Qubit).
• Automated DNA size selection by preparative electrophoresis (Pippin Prep).
• RNA extraction from biofluids (serum and plasma), addition of ERCC spike-in controls for RNA-seq, and robotic services for sample dilution and normalization in plates or tubes.

High content array based assays genotyping (Illumina Infinium). Full execution of assays including:

• Global DNA methylation (Infinium Methylation EPIC v2.0 / 850K)
• High-throughput SNP/CNV genotyping (Global Screening Array - GSA and Global Diversity Array - GDA-Cyto)

Capability to process many other commercial or consortium Infinium assays. Includes beadarray scanning, bisulfite conversion for methylation studies, and DNA restoration from paraffin-embedded samples (FFPE).

Automated NGS library preparation. Robotic construction of sequencing libraries with optimized protocols for high-fidelity RNA and DNA:

• Total RNA via ribodepletion (Polaris Watchmaker or Illumina Stranded Total RNA Ribo-Zero Ligated Anchors).
• mRNA via PolyA selection (Watchmaker).
• Small RNA (Small RNA NextFlex 4.0 Revvity).
• Preparation of indexed amplicons, exomes (Agilent SureSelect XT), and genomic DNA (Nextera-XT and Illumina DNA Flex).

Compatible with single-cell sequencing automation (Parse Biosciences and Illumina Single Cell). Possibility to generate NGS libraries for methylation analysis (BS-seq) and chromatin state (ATAC-seq, Umi4C).

Validation, quantification and genotyping by high-throughput qPCR: Custom robotic preparation of reactions in high-density plates (96 and 384 wells) for:

• Absolute quantification of NGS libraries using specific enzymatic assays (KAPA qPCR).
• Expression assays and microRNA profiling (TaqMan Advanced miRNA and Exiqon PCR panels), including automated cDNA synthesis.
• Single SNP genotyping using fluorogenic probes in 384-well format.

Standardised and custom bioinformatics analyses

Bulk differential expression and functional inference analysis (RNA-seq / Microarrays): Identification of expression profiles, pathway enrichment analysis, and gene ontology.

Single-cell transcriptomic analysis: scRNAseq (Chromium) and single-cell multi-omics including pseudobulk, clustering, UMAP, cell type annotation, differential expression at cell type and state level, and trajectory inference.

Spatial transcriptomics: Analysis of single-cell data with spatial component at single-cell or quasi-single cell level and 'STAMP', integrating histological information in 2D and 3D from NGS (Visium) and multiplex in situ (Xenium). Identification of niches and cell interactions.

Microtranscriptome analysis (XICRA Pipeline): Quantification using smallRNA-seq or microarrays of small non-coding RNAs (sncRNAs): piRNA, tRNA fragments (tRFs), microRNAs (miRNA) and sequence variants (isomiRs).

Global DNA methylation study: DNA methylation mapping using microarrays, analysis of differentially methylated regions (DMRs) and inference of methylation effects on gene expression, epigenetic clocks and cell deconvolution.

Genomic variation analysis (WGS, WES, panels, Microarrays): From whole genome (WGS), exome (WES), panels or SNP/CNV arrays, we study germline variants, their genetic association (GWAS) to phenotypes or clinical data, calculation of polygenic risk scores (PRS), and analysis of somatic variation, copy number alterations, LOH, and mutations associated with genetic diseases, cancer and treatment response or resistance.

Bacterial genomics and epidemiology (BacterialTyper Pipeline): Assembly, annotation and typing of complete bacterial genomes (WGS), applicable to outbreak identification and tracking.

Microbiome analysis: 16S + ITS metabarcoding, shotgun metagenomics and metatranscriptomics for microbiome characterization.

Multi-omics data integration: Combined mathematical modeling of genomic, transcriptomic, epigenomic, proteomic, metabolomic and clinical data.

Data science

Clinical and biomedical free-text analysis (AI/LLM): Natural language processing models applied to medical reports, electronic health records and scientific publications.

All services include support in data management and storage, preparation of figures and tables for publication, and submission of data to public repositories.