NGI Stockholm

National facility

NGI Stockholm (Production)

NGI Stockholm consists of two groups; Genomics Production and Genomics Applications Development, and offers state-of-the-art service in the rapidly developing field of massively parallel DNA sequencing.  Genomics Production offers library preparation and high-throughput sequencing followed by data processing and best practice analysis for a variety of well established applications. Genomics Production is Swedac accredited, which ensure that projects are completed in accordance with rigorous quality standards. Genomics Applications Development collaborates with researchers on applications not supported by Genomics Production, for more information see application list below.

Current status of operations for NGI Stockholm

SERVICES

  • DNA and RNA sequencing of user provided samples
  • Establishing novel sequencing applications addressing the needs of users
  • Outreach activities including provide guidelines and support for sample collections, study design and protocol selection

EQUIPMENT

  • Illumina HiSeq 2500
  • Illumina HiSeq X for whole genome re-sequencing
  • Illumina MiSeq for sequencing of small genomes and amplicons
  • Illumina cBot
  • Agilent Bravo
  • Agilent NGS Workstation
  • Agilent Bioanalyzer
  • Tecan Infinite 200 PRO
  • Caliper LabChip XT
  • Caliper LabChip GX
  • Bio-Rad CFX
  • Covaris
  • Fragment Analyzer
  • 10X Chromium for long-range haplotyping and de novo assembly
  • Oxford Nanopore MinION  for long-read sequencing (>10 kbp)

APPLICATIONS

Standard applications marked with a star (*) are currently performed by the Genomics Production and are ISO accredited. All other applications below are done by the Genomics Applications Development and are at different stages of initial testing, development and validation. These applications usually include a descriptive bioinformatic analysis (enquire for details). If you are interested in something not on this list, please let us know!

  • Human whole-genome sequencing (*) with best-practice bioinformatic analysis (see details)
  • Non-human whole-genome sequencing (*)
  • Strand-specific RNA sequencing (RNA-seq) (*) with best-practice bioinformatic analysis for supported genomes (see details)
  • Small RNA sequencing (*) with bioinformatic analysis. See Tech Note.
  • De novo genome sequencing (*) with best-practice bioinformatic analysis including 3-5 assemblies (see details)
  • Metagenomics (*)
  • Sequencing of finished library (*)
  • 10X Genomics Chromium for long range haplotyping and de novo assembly (see details of our first run)
  • Low input and FFPE RNA seq and bioinformatic analysis. Includes RNA and/or DNA extraction
  • ChIP seq bioinformatic analysis (see Tech Note)
  • ATAC seq with bioinformatic analysis
  • Bisulphite and oxidative bisulphite sequencing with bioinformatic analysis of whole human and non-model organism genomes
  • Cancer Analysis Workflow for identification of somatic variants bioinformatic analysis (see pipeline).
  • 20 kb mate pair libraries for de novo genome sequencing and translocation identification
  • RAD seq (reduced representation sequencing) and bioinformatic analysis for population genetics with bioinformatic analysis
  • User QC concept for low cost library preparation of microbial genomes (see tech note)
  • Exome and custom Agilent SureSelect capture
  • Custom sequence capture using Illumina and Roche/Nimblegen kits
  • Library preparation automation for large projects. See our Bravo protocol scripts on GitHub
  • Automation of large-scale bioinformatic analyses such as RNA-seq, smRNA-seq, ChIP-seq and Methyl-seq
  • Software development for quality control (MultiQC) and running small pipelines (Cluster Flow)

RECENT PROJECTS

  • Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.
  • MultiQC: Summarize analysis results for multiple tools and samples in a single report.
  • Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.
  • De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.
  • T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.
    • Grunewald J, Kaiser Y, Ostadkarampour M, Rivera NV, Vezzi F, Lötstedt B, Olsen RA, Sylwan L, Lundin S, Käller M, Sandalova T, Ahlgren KM, Wahlström J, Achour A, Ronninger M, Eklund A.
    • Eur Respir J. (2016) 47(3):898-909. doi: 10.1183/13993003.01209-2015 PMID: 26585430
  • The Norway spruce genome sequence and conifer genome evolution.
    • Nystedt B Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S.
    • Nature (2013) 497(7451):579-84. doi: 10.1038/nature12211 PMID: 23698360