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  • 1.
    Asp, Michaela
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Borgström, Erik
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Stuckey, Alexander
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Gruselius, Joel
    Carlberg, Konstantin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Andrusivova, Zaneta
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Salmén, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ståhl, Patrik
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Spatial Isoform Profiling within Individual Tissue SectionsManuscript (preprint) (Other academic)
    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.
    Fernandez Navarro, Jose
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Croteau, Deborah
    Jurek, Aleksandra
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Andrusivova, Zaneta
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Bohr, Vilhelm A
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Spatial Transcriptomics characterization of Alzheimer’s disease in the adult mouse brainManuscript (preprint) (Other academic)
    Abstract [en]

    Alzheimer’s disease (AD) is a devastating neurological disease associated with progressive loss of mental skills, cognitive and physical functions. Here, our goal was to uncover novel and known molecular targets in the structured layers of the hippocampus and olfactory bulbs that may contribute to hippocampal synaptic dysfunction and smelling defects in AD mice. Spatial Transcriptomics was used to identify high confidence genes that were differentially regulated in AD mice relative to controls. A discussion of how these genes may contribute to AD pathology is provided.

  • 3.
    Maniatis, Silas
    et al.
    New York Genome Ctr, Ctr Genom Neurodegenerat Dis, New York, NY 10013 USA..
    Aijo, Tarmo
    Flatiron Inst, Ctr Computat Biol, New York, NY 10010 USA..
    Vickovic, Sanja
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Braine, Catherine
    New York Genome Ctr, Ctr Genom Neurodegenerat Dis, New York, NY 10013 USA.;Columbia Univ, Mortimer B Zuckerman Mind Brain Behav Inst, New York, NY 10032 USA..
    Kang, Kristy
    New York Genome Ctr, Ctr Genom Neurodegenerat Dis, New York, NY 10013 USA..
    Mollbrink, Annelie
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fagegaltier, Delphine
    New York Genome Ctr, Ctr Genom Neurodegenerat Dis, New York, NY 10013 USA..
    Andrusivova, Zaneta
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Saarenpaa, Sami
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Saiz-Castro, Gonzalo
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Cuevas, Miguel
    Columbia Univ, Mortimer B Zuckerman Mind Brain Behav Inst, New York, NY 10032 USA..
    Watters, Aaron
    Flatiron Inst, Ctr Computat Biol, New York, NY 10010 USA..
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Bonneau, Richard
    Flatiron Inst, Ctr Computat Biol, New York, NY 10010 USA.;NYU, Ctr Data Sci, New York, NY 10011 USA..
    Phatnani, Hemali
    New York Genome Ctr, Ctr Genom Neurodegenerat Dis, New York, NY 10013 USA.;Columbia Univ, Mortimer B Zuckerman Mind Brain Behav Inst, New York, NY 10032 USA..
    Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis2019In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 364, no 6435, p. 89-+Article in journal (Refereed)
    Abstract [en]

    Paralysis occurring in amyotrophic lateral sclerosis (ALS) results from denervation of skeletal muscle as a consequence of motor neuron degeneration. Interactions between motor neurons and glia contribute to motor neuron loss, but the spatiotemporal ordering of molecular events that drive these processes in intact spinal tissue remains poorly understood. Here, we use spatial transcriptomics to obtain gene expression measurements of mouse spinal cords over the course of disease, as well as of postmortem tissue from ALS patients, to characterize the underlying molecular mechanisms in ALS. We identify pathway dynamics, distinguish regional differences between microglia and astrocyte populations at early time points, and discern perturbations in several transcriptional pathways shared between murine models of ALS and human postmortem spinal cords.

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