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

APPLICATIONS

These standard applications are currently performed by the Genomics Production and are ISO accredited:

• 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. Low input by GAD.
• De novo genome sequencing with best-practice bioinformatic analysis including 3-5 assemblies (see details). Multi-library assembly by GAD.
• Metagenomics
• Sequencing of finished library

The following applications are handled 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!

• 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
• Low input smRNAseq and bioinformatic analysis. Includes RNA and/or DNA extraction
• ChIP seq bioinformatic analysis (see Tech Note)
• ATAC seq with bioinformatic analysis
• HiC for de-novo genome scaffolding and epigenetics studies
• Bisulphite and oxidative bisulphite sequencing with bioinformatic analysis of whole human and non-model organism genomes
• Sarek 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
• De-novo multi-library assembly bioinformatic analysis
• 16S and custom amplicon automated library preparation and sequencing
• User QC concept for low cost library preparation of microbial genomes (see tech note)
• 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)

EQUIPMENT

• Illumina NovaSeq
• Illumina HiSeq X for whole genome re-sequencing
• Illumina HiSeq 2500
• 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)

RECENT PROJECTS

• Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements
  • J Eisfeldt, M Pettersson, F Vezzi, J Wincent, M Käller, J Gruselius, D Nilsson, ES Lundberg, CMB Carvalho, A Lindstrand
  • PLoS Genomics (2019); doi: 10.1371/journal.pgen.1007858 PMID: 30735495
• First de novo whole genome sequencing and assembly of the pink-footed goose
  • J.M.Pujolar, L.Dalén, R.A.Olsen, M.M.Hansen, J.Madsen
  • Genomics (2017); doi: 10.1016/j.ygeno.2017.08.008 PMID: 28860085
• Cluster Flow: A user-friendly bioinformatics workflow tool
  • Ewels P, Krueger F, Käller M, Andrews S.
  • F1000Research (2016), 5:2824. doi: 10.12688/f1000research.10335.2 PMID: 28299179
• Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.
  • Engström K, Wojdacz TK, Marabita F, Ewels P, Käller M, Vezzi F, Prezza N, Gruselius J, Vahter M, Broberg K.
  • Arch Toxicol. (2016). doi: 10.1007/s00204-016-1879-4 PMID: 27838757
• MultiQC: Summarize analysis results for multiple tools and samples in a single report.
  • Ewels P, Magnusson M, Lundin S, Käller M.
  • Bioinformatics (2016) 32 (19): 3047-3048. doi: 10.1093/bioinformatics/btw354 PMID: 27312411
• Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.
  • Ivanov M, Kals M, Lauschke V, Barragan I, Ewels P, Käller M, Axelsson T, Lehtiö J, Milani L, Ingelman-Sundberg M.
  • Nucleic Acids Res. (2016) 44(14):6756-69. doi: 10.1093/nar/gkw316 PMID: 27131363
• De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.
  • Olsen RA, Bunikis I, Tiukova I, Holmberg K, Lötstedt B, Pettersson OV, Passoth V, Käller M, Vezzi F.
  • Gigascience (2015) 4:56. doi: 10.1186/s13742-015-0094-1 PMID: 26617983
• 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