Spatial Multimodal Analysis (SMA) - Spatial Transcriptomics
type: Dataset
description: This dataset contains Spatial Transcriptomics (ST) data matching with Matrix Assisted Laser Desorption/Ionization - Mass Spetrometry Imaging (MALDI-MSI). This data is complementary to data contained in the same project. FIles with the same identifiers in the two datasets originated from the very same tissue section and can be combined in a multimodal ST-MSI object. For more information about the dataset please see our manuscript posted on BioRxiv (doi: https://doi.org/10.1101/2023.01.26.525195). This dataset includes ST data from 19 tissue sections, including human post-mortem and mouse samples. The spatial transcriptomics data was generated using the Visium protocol (10x Genomics). The murine tissue sections come from three different mice unilaterally injected with 6-OHDA. 6-OHDA is a neurotoxin that when injected in the brain can selectively destroy dopaminergic neurons. We used this mouse model to show the applicability of the technology that we developed, named Spatial Multimodal Analysis (SMA). Using our technology on these mouse brain tissue sections we were able to detect both dopamine with MALDI-MSI and the corresponding gene expression with ST. This dataset includes also one human post-mortem striatum sample that was placed on one Visium slide across the four capture areas. This sample was analyzed with a different ST protocol named RRST (Mirzazadeh, R., Andrusivova, Z., Larsson, L. et al. Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nat Commun 14, 509 (2023). https://doi.org/10.1038/s41467-023-36071-5), where probes capturing the whole transcriptome are first hybridized in the tissue section and then spatially detected. Each tissue section contained in the dataset has been given a unique identifier that is composed of the Visium array ID and capture area ID of the Visium slide that the tissue section was placed on. This unique identifier is included in the file names of all the files relative to the same tis…
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Marco Vicari
creator: Reza Mirzazadeh
  type: Person
  family name: Mirzazadeh
  given name: Reza
creator: Anna Nilsson
  type: Person
  family name: Nilsson
  given name: Anna
creator: Patrik Bjärterot
creator: Ludvig Larsson
  type: Person
  family name: Larsson
  given name: Ludvig
creator: Hower Lee
  type: Person
  family name: Lee
  given name: Hower
creator: Mats Nilsson
  type: Person
  family name: Nilsson
  given name: Mats
creator: Julia Foyer
  type: Person
  family name: Foyer
  given name: Julia
creator: Markus Ekvall
  type: Person
  family name: Ekvall
  given name: Markus
creator: Paulo Czarnewski
  type: Person
  family name: Czarnewski
  given name: Paulo
creator: Xiaoqun Zhang
  type: Person
  family name: Zhang
  given name: Xiaoqun
creator: Per Svenningsson
  type: Person
  family name: Svenningsson
  given name: Per
creator: Per Andrén
creator: Lukas Käll
  type: Person
  family name: Käll
  given name: Lukas
creator: Joakim Lundeberg
  type: Person
  family name: Lundeberg
  given name: Joakim
date modified: 2023-05-16
date published: 2023-05-16
keywords: Medical and Health Sciences
  type: DefinedTerm
  term code: 3
keywords: Genetics and Genomics
  type: DefinedTerm
  term code: 10609
keywords: Gene expression (incl. microarray and other genome-wide approaches)
keywords: Genomics
keywords: Genomics and transcriptomics
license: https://creativecommons.org/licenses/by/4.0/
publisher: Royal Institute of Technology
version: 0

PropertyValue
property ID: DOI
value: 10.17044/SCILIFELAB.22778920

Marco Vicari
type: Person
affiliation: Science for Life Laboratory
family name: Vicari
given name: Marco

Science for Life Laboratory
type: Organization

Patrik Bjärterot
type: Person
affiliation: Science for Life Laboratory
family name: Bjärterot
given name: Patrik

Per Andrén
type: Person
affiliation: Science for Life Laboratory
family name: Andrén
given name: Per

Royal Institute of Technology
type: Organization