National Genomics Infrastructure – Uppsala

NGI Uppsala offers next generation sequencing (NGS) and genotyping services of high quality using the latest technologies to academic researchers in Sweden and abroad.

NGI Uppsala consists of two units, the SNP&SEQ Technology Platform and Uppsala Genome Center. Our goal is to provide researchers in Sweden and abroad cost effective, flexible and expedient service.

Our wide-range of Next Generation Sequencing (NGS) services include short-read technologies using Illumina and IonS5XL instruments and long-read technologies using PacBio Sequel, Sequel II and Oxford Nanopore PromethION. Single-cell applications using the 10x Genomics system and protein analysis using the Olink Explore assay is also offered in combination with short-read Illumina sequencing. Our services cover a unique range of applications and solutions in the field of genomics. We also undertake technically challenging projects that can lead to development of novel NGS protocols and applications.

For genotyping we assist projects on all scales (up to 5 million SNPs per sample) in a few to thousands of samples using Illumina iScan system.

DNA-methylation profiling is offered by array-based SNP genotyping and by whole-genome and targeted bisulfite sequencing using Illumina technology. Methylation profiling is also possible on native DNA using PacBio Sequel.

Extraction of ultra High Molecular Weight (uHMW) DNA is offered for de novo projects to be sequenced using PacBio or Oxford Nanopore technologies.

The SNP genotyping and sequencing using Illumina technologies are accredited by SWEDAC according to the ISO/IEC 17025 quality standard.

The best set up for a particular project depends on several factors e.g. research question, amount, quality and number of samples to be analyzed, as well as the requested amount of data. Read more about our services and technologies below, or visit our website for a for a full list of the services that we offer: https://ngisweden.scilifelab.se/

Services

Short read NGS with:	NovaSeq6000, MiSeq, iSeq (Illumina) IonS5XL (ThermoFisher)
Long read NGS with:	PacBio Sequel, Sequel II & IIe and Oxford Nanopore PromethION
Genotyping on small to genome wide scale with:	iScan (Illumina)
Methylation profiling with:	iScan (Illumina), NovaSeq 6000 (Illumina), PacBio Sequel and Sequel II
High-throughput protein biomarker analysis with:	Olink Explore and NovaSeq 6000 (Illumina)

Our services include:

• Technical support for sequencing and genotyping projects design.
• Quality control of samples before genotyping and sequencing.
• Extraction of ultra HMW DNA for long-read sequencing.
• Library preparation for sequencing with protocols optimal for each research project.
• Quality control of sequencing and genotyping data.
• Compilation of materials and methods for publications.
• Bioinformatics support, including:
  • data delivery including quality information via SNIC-UPPMAX.
  • automated bioinformatics analyses in a number of applications such as human WGS and WES, RNA-seq (Illumina sequencing).
  • de novo assembly of PacBio data.

Applications

Sequencing

• Whole genome sequencing for analysis of genetic variation
• Whole exome sequencing for analysis of genetic variation
• Whole genome de novo sequencing
• Whole-genome bisulphite sequencing for DNA methylation analysis
• Whole transcriptome sequencing (RNA-seq)
• Single-cell sequencing (including RNA-seq, ATAC-seq, combined profiling of gene expression and proteins)
• Targeted sequencing of genomic regions (amplicon or hybrid capture sequencing)
• Chromatin immunoprecipitation sequencing (ChIP-seq)
• High-throughput protein biomarker analysis (Olink Explore assay)
• Sequencing of premade libraries
• Sequencing of covid-19 samples using Nanopore and IonTorrent technologies

Genotyping

• SNP genotyping on all scales in various organisms
• Custom designed SNP panels
• Copy number variation
• Genome-wide DNA methylation analysis

Equipment

• 2X iScan (Illumina)
• 2X NovaSeq 6000 sequencers (Illumina)
• 2X MiSeq sequencer (Illumina)
• 1X iSeq 100 sequencer (Illumina)
• 1X Chromium system (10X Genomics)
• 1X PacBio Sequel system (Pacific Biosciences)
• 1X PacBio Sequel II system (Pacific Biosciences)
• 1X PacBio Sequel IIe system (Pacific Biosciences)
• 1X Oxford Nanopore PromethION
• 1X Ion S5XL (Thermo Fisher)
• Liquid handling robots for automated workflows
• Instruments for high-throughput and accurate quality control of DNA/RNA

Using the unit

For more information about the NGI nodes in Uppsala, visit the node-specific websites:

SNP&SEQ Technology Platform (Genotyping and Illumina sequencing)

Uppsala Genome Center (PacBio, Ion, Oxford Nanopore)