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  • 1.
    Asp, Michaela
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Borgström, Erik
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Stuckey, Alexander
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Gruselius, Joel
    Carlberg, Konstantin
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Andrusivova, Zaneta
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Salmén, Fredrik
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ståhl, Patrik
    Lundeberg, Joakim
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Spatial Isoform Profiling within Individual Tissue SectionsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Spatial Transcriptomics has been shown to be a persuasive RNA sequencing

    technology for analyzing cellular heterogeneity within tissue sections. The

    technology efficiently captures and barcodes 3’ tags of all polyadenylated

    transcripts from a tissue section, and thus provides a powerful platform when

    performing quantitative spatial gene expression studies. However, the current

    protocol does not recover the full-length information of transcripts, and

    consequently lack information regarding alternative splice variants. Here, we

    introduce a novel protocol for spatial isoform profiling, using Spatial

    Transcriptomics barcoded arrays.

  • 2.
    Borgström, Erik
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Redin, David
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundin, Sverker
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Berglund, Emelie
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ahmadian, Afshin
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Phasing of single DNA molecules by massively parallel barcoding2015Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, artikkel-id 7173Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.

  • 3.
    Hard, Joanna
    et al.
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Al Hakim, Ezeddin
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Kindblom, Marie
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Bjorklund, Asa K.
    Uppsala Univ, Dept Cell & Mol Biol, Natl Bioinformat Infrastruct Sweden, Scilifelab, Uppsala, Sweden..
    Sennblad, Bengt
    Uppsala Univ, Dept Cell & Mol Biol, Natl Bioinformat Infrastruct Sweden, Scilifelab, Uppsala, Sweden..
    Demirci, Ilke
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Paterlini, Marta
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Reu, Pedro
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Borgström, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Stahl, Patrik L.
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Michaelsson, Jakob
    Karolinska Inst, Dept Med, Ctr Infect Med, Huddinge, Sweden..
    Mold, Jeff E.
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Frisen, Jonas
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing2019Inngår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 20, artikkel-id 68Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Comparing the performance of Conbase to three other methods, we find that Conbase performs best in terms of false discovery rate and specificity and provides superior robustness on simulated data, in vitro expanded fibroblasts and clonal lymphocyte populations isolated directly from a healthy human donor.

  • 4.
    Redin, David
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Frick, Tobias
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Aghelpasand, Hooman
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Borgström, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Olsen, Remi-Andre
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Box 1031, S-17121 Solna, Sweden..
    Ahmadian, Afshin
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    High throughput barcoding method for genome-scale phasing2019Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikkel-id 18116Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The future of human genomics is one that seeks to resolve the entirety of genetic variation through sequencing. The prospect of utilizing genomics for medical purposes require cost-efficient and accurate base calling, long-range haplotyping capability, and reliable calling of structural variants. Short-read sequencing has lead the development towards such a future but has struggled to meet the latter two of these needs. To address this limitation, we developed a technology that preserves the molecular origin of short sequencing reads, with an insignificant increase to sequencing costs. We demonstrate a novel library preparation method for high throughput barcoding of short reads where millions of random barcodes can be used to reconstruct megabase-scale phase blocks.

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