NGI Stockholm (Genomics Applications)

National facility

NGI Stockholm (Production)

The Genomics Applications facility offers state-of-the-art service in the rapidly developing field of massively parallel DNA sequencing (MPS).

SERVICES

  • Carry out customer projects for applications not supported by the Genomics Production facility.
  • Establishing novel sequencing applications addressing the needs of customers.
  • Outreach activities including provide guidelines and support for sample collections, study design and protocol selection.

EQUIPMENT

  • Optical mapper. OpGen Argus.
  • The facility has full access to the instrumentation of the Genomics Production Facility.

APPLICATIONS

The major function of the facility is to establish and automate new sequencing applications with corresponding bioinformatic analysis requested by the users. Below is a list of applications currently performed by the Genomics Applications facility (please refer to Genomics Production Facility for the standard applications):

  • Optical mapping using OpGen Argus.
  • Mate-pair sequencing of 2-8 kb inserts.
  • De novo assembly.
  • DNA library preparation using:
    • Illumina TruSeq PCR-free for reduced GC%-bias.
    • Rubicon ThruPLEX for small amounts of DNA  and ChIP-seq.
    • Illumina Nextera XT for microbial genomes and PCR-products.
    • Reduced representation libraries for SNP discovery.
  • Exome and custom sequence capture using:
    • Roche Nimblegen EZ capture.
    • Illumina Nextera rapid capture.
    • Agilent Haloplex capture.
  • RNA libraries:
    • Small RNA library preparation and bioinformatic analysis.
    • rRNA depletion using Ribozero (Illumina and Epicenter).
    • Small amounts of RNA input (See our Technical Note and presentation).
  • Agilent SureSelect methyl-seq enrichment

 

RECENT PROJECTS

  • 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 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.De Novo SNP
  • Discovery in the Scandinavian Brown Bear (Ursus arctos). Norman AJ, Street NR, Spong G.PLoS One. 2013 Nov 18;8(11):e81012
  • Chemical fragmentation for massively parallel sequencing library preparation. Gyarmati P, Song Y, Hällman J, Käller M. J Biotechnol. 2013 Oct 10;168(1):95-100. doi: 10.1016/j.jbiotec.2013.08.020. Epub 2013 Aug 27.
  • Automation, validation and technology transfer of stranded RNA and ribozero library preparation methods to Genomics  Production Facility.
  • Automation, validation and technology transfer of PCR-free and Rubicon thruplex methods for unbiased and low input amount DNA library preparation to Genomics Production Facility.