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 facilities, the SNP&SEQ Technology Platform and Uppsala Genome Center. Our aim 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 and Oxford Nanopore PromethION. Single-cell applications using the 10x Genomics system is also offered in combination with short-read Illumina sequencing. Thus 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, from 1 to millions of SNPs per sample in a few to thousands of samples using Illumina iScan and Agena MassARRAY systems.

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.

The SNP genotyping and sequencing using Illumina, Ion and PacBio 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

Our services include:

• Technical support for sequencing and genotyping projects design.
• Quality control of samples before genotyping and 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:
  • delivery of sequence reads with 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 with HGAP or FALCON assembler.

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)
• Sequencing of premade libraries

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)
• 1X MassARRAY (Agena Bioscience) _{^{*Will be phased out and removed from our service during fall 2020}}
• 1X Hidex Sense (Hidex Oy)
• 2X NovaSeq6000 sequencers (Illumina)
• 2X MiSeq sequencer (Illumina)
• 1X iSeq sequencer (Illumina)
• 1X Chromium system (10X Genomics)
• 1X PacBio Sequel II system (Pacific Biosciences)
• 2X PacBio Sequel system (Pacific Biosciences)
• 1X Oxford Nanopore PromethION
• 1X Ion S5XL (IonS5XL, Thermo Fisher)
• Liquid handling robots for automated workflows
• Instruments for high-throughput and accurate quality control of DNA/RNA

Using the facility

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)