SciLifeLab, Uppsala University

Founded in 1477, Uppsala University (UU) is one of the oldest universities in Europe. It is a large university with nearly 44,000 students and 7,000 employees. UU is a complete university with research and educational programs in all scientific disciplines.

Science for Life Laboratory is a distributed national center for molecular biosciences at four collaborating Swedish universities: Stockholm University, Karolinska Institutet, KTH Royal Institute of Technology and Uppsala University. The National Genomics Infrastructure (NGI) constitutes a major part of the SciLifeLab Genomics platform. Significant efforts are made by SciLifeLab Genomics to evaluate emerging technologies and to develop novel methods in the rapidly changing field of genomics to enable internationally competitive genomic research in Sweden.

The NGI facilities at SciLifeLab Genomics offer a unique combination of consultative support for project design and executive support for sequencing or genotyping and basic data analysis for a variety of applications in disease genetics and evolutionary biology.

The SNP&SEQ Technology Platform at NGI/SciLifeLab Genomics in Uppsala is well equipped with the most modern technologies for projects on all scales, from genotyping single SNPs to whole-genome sequencing, bisulfite sequencing, transcriptome, targeted and single-cell sequencing. For data analysis and storage the SciLifeLab Genomics facilities and its users have access to SNIC-UPPMAX (Uppsala Multidisciplinary Centre for Advanced Computational Sciences, which is a national resource for high-performance computing.

NGI Uppsala SNP&SEQ Technology Platform will contribute to EASI-Genomics by providing Transnational Access to 3’- and 5’-single-cell transcriptome sequencing, epigenetic sequencing, including low input DNA epigenetic sequencing, and de novo long-range sequencing of mammalian-sized genomes. The Chromium technology (10x Genomics) and Nadia system (Dolomite Bio), and short-read sequencing using Illumina sequencers will mainly be used for these applications. 

Technical equipment and infrastructure

NGI Uppsala SNP&SEQ Technology Platform offers sequencing on all scales, using 2 NovaSeq, 5 Illumina HiSeqX, 1 HiSeq2500,1 MiSeq and 1 iSeq sequencing instruments, and genotyping using 2 iScan instruments, and one Agena Mass Array instrument. The core instruments for sequencing and genotyping are supported by 8 liquid handling work stations (Hamilton, Tecan, BiomekFX, Janus) and auxiliary equipment, like sonicators, PCR machines, fluorometers for  DNA concentration measurements etc.

With its modern technologies, the SNP&SEQ Facility is equipped for assisting projects on all scales with a comprehensive range of genomic applications from genotyping of single SNPs to genome wide resolution, as well as whole genome-, bisulfite-, RNA-, targeted and single cell-sequencing for a wide variety of organisms. The majority of the highly automated laboratory procedures and data processing workflows at the SNP&SEQ Facility is accredited by Swedac according to the ISO/IEC 17025 quality standard. The Scope of Accreditation can be found on the SNP&SEQ homepage (link below). The staff of the NGI Uppsala SN&SEQ Technology Platform consists of 40 FTEs, including laboratory personnel, project- and lab-coordinators, systems developers, and bioinformaticians.

UPPMAX is a high-performance compute cluster and storage facility located at Uppsala University that supports the NGI/SciLifeLab sequencing operations. The production cluster, specifically dedicated to data-intensive computational analyses of e.g. human whole-genome sequencing data, consists of 250 nodes, each with dual 8-core CPUs (4000 cores in total) and 256 Gb RAM. Scientists needing to process sensitive human data, can have access to a cluster with 200 dual 8-core CPUs (3200 cores in total) and 128 Gb of RAM (nodes with 256 and 512 Gb RAM are available). Users of the UPPMAX clusters are not only given access to hardware resources but also a toolbox with programs for DNA sequence data analyses. 

Uppsala Universitet