Available Services

Whole Genome Sequencing (WGS) is a comprehensive and high-throughput technique that enables the complete DNA sequence of an organism’s entire genome. WGS is a powerful tool with applications in various fields, including genomics research, personalized medicine, and clinical diagnostics. It provides a comprehensive view of an organism’s genetic makeup, enabling a deeper understanding of genetic variations, evolution, and the genetic basis of diseases.

Bioinformatic analysis of WGS data can be provided as a combined service by the National Facility for Data Handling and Analysis. Please select: SID: NF62.02.01

Whole Exome Sequencing (WES) is a targeted sequencing approach that focuses on sequencing the protein-coding regions of the genome, known as the exome. The exome comprises the exons, which are the coding regions of genes, and represents only a small fraction (about 1-2%) of the entire genome. Despite this, the exome contains most known disease-causing mutations, making WES a cost-effective alternative to Whole Genome Sequencing (WGS) for many applications. WES is widely used in both clinical and research settings. In clinical genetics, it is employed for diagnosing genetic disorders, identifying causative mutations, and understanding the genetic basis of rare diseases. In research, WES is valuable for studying the genetics of complex traits and diseases.

Visium HD Spatial Gene Expression (10X Genomics) and the Visium Spatial Gene Expression for Fresh Frozen (Direct placement) allow the spatial profiling of gene expression within intact tissue sections. The protocols allow for the analysis of gene expression while preserving the spatial context of cells within a tissue sample.

Total RNA sequencing is a powerful and widely used molecular biology technique that aims to analyse and quantify the entire transcriptome of a biological sample. The transcriptome represents the complete set of RNA molecules, including messenger RNA (mRNA), and non-coding RNAs, present in a cell or tissue. Total RNA sequencing provides a comprehensive view of the transcriptome, allowing researchers to gain insights into gene expression patterns, identify novel transcripts, and understand the regulatory mechanisms underlying various biological processes.

Small RNA sequencing is a specialized technique designed to analyse and profile small RNA molecules present in a biological sample. Small RNAs are short RNA molecules, typically ranging from 18 to 30 nucleotides in length, and they play essential roles in various cellular processes, including gene regulation, RNA silencing, and post-transcriptional control. Small RNA sequencing is widely used to study the expression profiles of miRNAs and other small RNAs, providing valuable insights into their roles in gene regulation, development, and disease.

Single-cell multiome ATAC + Gene Expression is a cutting-edge technology that enables the simultaneous profiling of chromatin accessibility and gene expression at the single-cell level, providing a comprehensive view of the molecular landscape within individual cells. This technology is widely used in various biological research areas, including understanding cellular diversity in tissues, identifying cell types and states, deciphering regulatory networks, and gaining insights into how chromatin accessibility relates to gene expression at the single-cell level.

Single-cell immune profiling with 10x Genomics technology is a powerful method for 5’ RNA sequencing at the single-cell level and to profile at the same time the T-cells and/or B-cells receptors at single cell level by sequencing the V(D)J regions.

Single-cell ATAC sequencing with the 10X Genomics platform involves profiling the chromatin accessibility of individual cells/nuclei at a high resolution. The assay, commonly known as scATAC-seq (Single-cell Assay for Transposase-Accessible Chromatin sequencing), utilizes the 10X Genomics Chromium system to barcode and index individual nuclei, it provides valuable insights into the epigenomic landscape of individual cells, allowing researchers to study cellular heterogeneity and regulatory processes at high resolution.

Single-cell 3′ RNA sequencing with 10x Genomics technology is a powerful method for studying gene expression at the single-cell level. It enables the profiling of thousands to tens of thousands of single cells in parallel. It captures heterogeneity within cell populations, allowing the identification of rare cell types and subpopulations. It reveals differences in gene expression between individual cells, providing a more nuanced understanding of cellular diversity.

The Fixed RNA Profiling assay, also called the Single Cell Gene Expression Flex assay by 10X Genomics, is a way to prepare single cell RNA-seq libraries from formaldehyde-fixed cells and tissues as well as FFPE tissue blocks (please consider that from FFPE tissues the isolated population primarily consists of nuclei suspension, thus the RNA-seq analysis is to be intended at nuclear level). This process allows researchers to lock in the biological state of their samples at the time of fixation and store the fixed cell suspension for at least 6 months at -80°C.

The National Facility for Genomics will provide sequencing of pools of libraries prepared by the users with the NovaSeq6000 sequencing platform (Illumina).

The NovaSeq 6000 is a high-throughput sequencing platform developed by Illumina. It’s designed to handle a wide range of applications and large-scale genomic projects.

NovaSeq 6000 is commonly used for: Whole Genome Sequencing (WGS), Exome Sequencing (WES), Transcriptome Analysis (bulk RNA-Seq or single-cell RNAseq), Metagenomics, Epigenomics studies, Population Genomics.

The National Facility for Genomics will provide sequencing of pools of libraries prepared by the users with the NextSeq2000 sequencing platform (Illumina).

The NextSeq 2000 is a next-generation sequencing platform developed by Illumina. It is designed to offer high-throughput sequencing with flexibility for various applications.

The NextSeq 2000 is commonly used for: Whole Genome Sequencing (WGS), RNA Sequencing (RNA-Seq and single-cell RNA-seq), Targeted Sequencing (amplicon sequencing), Exome Sequencing (WES), Metagenomics, ChIP-Seq and Epigenomics.

The National Facility for Genomics will provide sequencing of pools of libraries prepared by the users with the MiSeq sequencing platform (Illumina).

the MiSeq is a benchtop next-generation sequencing platform developed by Illumina. It’s designed for smaller-scale sequencing projects and offers flexibility for various applications.

MiSeq is commonly used for: Targeted Sequencing (amplicon sequencing), Small Genomes Sequencing, Metagenomics, 16S rRNA Sequencing, Small RNA-Seq, Viral genomes Sequencing.

Nanopore sequencing of small gDNAs will be performed with the native barcoding kit that refers to a set of reagents and protocols designed to enable the simultaneous sequencing of multiple samples by adding unique barcodes to each sample before sequencing. This approach is particularly useful for studying small bacteria genomes (gDNA) as it allows for high-throughput sequencing and analysis of multiple samples using a single flowcell.

This approach provides a cost-effective and efficient way to sequence multiple small bacteria genomes simultaneously, making it a valuable tool in microbiome studies, environmental monitoring, and other applications in microbial genomics.

Nanopore sequencing is a next-generation sequencing technology that uses nanopores to directly sequence DNA molecules and to analyse DNA bases modifications. This method is known for producing long reads, and in some cases, ultra-long reads, making it valuable for various genomic applications.

Direct RNA Sequencing with Nanopore technology is a cutting-edge method for sequencing RNA molecules without the need for conversion to complementary DNA (cDNA) as required in traditional RNA sequencing methods. The protocol involves the direct sequencing of RNA strands through nanopores, allowing for the real-time detection of RNA sequences and RNA bases modifications. Direct RNA Sequencing with Nanopore technology offers the advantage of studying RNA molecules in their native state, providing valuable insights into RNA processing, alternative splicing, and modifications without the need for reverse transcription. It is particularly valuable for capturing the full complexity of the transcriptome.

Cell-free DNA (cfDNA) sequencing with Nanopore technology represents a revolutionary approach to interrogate the genetic information present in circulating DNA, often extracted from blood plasma. Unlike traditional sequencing methods, this protocol allows for the direct sequencing of cfDNA without the need for intermediate steps such as PCR amplification or conversion and allows the analysis in real time of the methylation status of circulating cfDNA. Its applications extend to clinical diagnostics, providing valuable information for personalized medicine and disease monitoring such as liquid biopsy for cancer detection, monitoring treatment response, and identifying minimal residual disease.

Nanopore cDNA sequencing is a powerful technique that combines the benefits of nanopore sequencing technology with the study of complementary DNA (cDNA), which represents the transcribed RNA in a biological sample. This method allows researchers to investigate gene expression, alternative splicing, and other aspects of RNA biology with long-read sequencing capabilities. Nanopore cDNA sequencing offers several advantages, including the ability to generate long reads that span entire transcripts. This makes it particularly valuable for studying complex transcriptomes, characterizing novel isoforms, and exploring the dynamics of gene expression in various biological contexts.

Methylation sequencing (Methyl-seq) is a technique used to study DNA methylation, a key epigenetic modification where methyl groups are added to DNA molecules, typically at cytosine bases in CpG sites. This method allows researchers to identify and quantify methylation patterns across the genome, providing insights into gene regulation, cellular differentiation, development, and disease processes such as cancer, where abnormal methylation often occurs.

The GeoMx Digital Spatial Profiling service provides cutting-edge technology for spatially resolved gene expression and protein analysis. This service supports fresh-frozen (FF), fixed-frozen and formalin-fixed, paraffin-embedded (FFPE) tissue samples, enabling researchers to explore spatial biology in diverse sample types.

Microbiome analysis using 16S and ITS amplicon sequencing is a widely used technique to study the composition and diversity of microbial communities, particularly bacteria and fungi. The 16S ribosomal RNA (rRNA) gene is a molecular marker found in the genomes of bacteria and archaea, and its variable regions are commonly used for taxonomic classification, while ITS is used to profile fungal communities. Microbiome analysis using 16S and ITS amplicon sequencing is valuable in a range of fields, including environmental science, human health, agriculture, and more. It provides a cost-effective way to characterize microbial communities and understand their roles in various ecosystems or host-associated environments.