Technology development
Within the research group we work a lot with method development of different -omic methods.
Project description
Our ability to perform large-scale studies of a number of the key molecular players such as DNA, RNA, protein and cellular metabolites has greatly advanced our ability to understand complex biological systems. Analysis of combinations of of DNA, RNA and protein data, i.e. multi-omics data, provide the basis of large-scale data driven biology and medicine. Recent rapid progress in data-driven science has been enabled through a combination of high-throughput large-scale laboratory methods and development of sophisticated bioinformatics analyses. In this project we aim to improve upon existing and develop new technology solutions which enable large-scale multi-omics analyses using next generation DNA sequencing (NGS).
Collaborating partners
- Ann-Christin Wiman, NGI/SNP&SEQ Technology Platform, SciLifeLab Genomics, Uppsala
- Claudia Bergin, MSCG unit, SciLifeLab Genomics, Uppsala
Selected publications
Hård J, Mold JE, Eisfeldt J, Tellgren-Roth C, Häggqvist S, Bunikis I, Contreras-Lopez O, Chin CS, Nordlund J, Rubin CJ, Feuk L, Michaëlsson J, Ameur A. Long-read whole-genome analysis of human single cells. Nat Commun. 2023 Aug 24;14(1):5164. doi: 10.1038/s41467-023-40898-3. PubMed PMID: 37620373; PubMed Central PMCID: PMC10449900.
Raine A, Lundmark A, Annett A, Wiman AC, Cavalli M, Wadelius C, Bergin C, Nordlund J.scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation. Sci Rep. 2022 Apr 6;12(1):5772. doi: 10.1038/s41598-022-09798-2. PubMed PMID: 35388090; PubMed Central PMCID: PMC8986790.
Han Y, Zheleznyakova GY, Marincevic-Zuniga Y, Kakhki MP, Raine A, Needhamsen M, Jagodic M. Comparison of EM-seq and PBAT methylome library methods for low-input DNA. Epigenetics. 2022 Oct;17(10):1195-1204. doi: 10.1080/15592294.2021.1997406. Epub 2021 Nov 17. PMID: 34709110; PMCID: PMC9542412.
Raine A, Liljedahl U, Nordlund J. Data quality of whole genome bisulfite sequencing on Illumina platforms. PLoS One. 2018;13(4):e0195972. doi: 10.1371/journal.pone.0195972. eCollection 2018. PubMed PMID: 29668744; PubMed Central PMCID: PMC5905984.
Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J. SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing. Nucleic Acids Res. 2017 Apr 7;45(6):e36. doi: 10.1093/nar/gkw1110. PubMed PMID: 27899585; PubMed Central PMCID: PMC5389478.