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Träfflista för sökning "AMNE:(NATURAL SCIENCES Biological Sciences Biochemistry and Molecular Biology) ;pers:(Nilsson Mats);pers:(Wählby Carolina)"

Sökning: AMNE:(NATURAL SCIENCES Biological Sciences Biochemistry and Molecular Biology) > Nilsson Mats > Wählby Carolina

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1.
  • Marco Salas, Sergio, et al. (författare)
  • De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks
  • 2022
  • Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 18:8
  • Tidskriftsartikel (refereegranskat)abstract
    • With the emergence of high throughput single cell techniques, the understanding of the molecular and cellular diversity of mammalian organs have rapidly increased. In order to understand the spatial organization of this diversity, single cell data is often integrated with spatial data to create probabilistic cell maps. However, targeted cell typing approaches relying on existing single cell data achieve incomplete and biased maps that could mask the true diversity present in a tissue slide. Here we applied a de novo technique to spatially resolve and characterize cellular diversity of in situ sequencing data during human heart development. We obtained and made accessible well defined spatial cell-type maps of fetal hearts from 4.5 to 9 post conception weeks, not biased by probabilistic cell typing approaches. With our analysis, we could characterize previously unreported molecular diversity within cardiomyocytes and epicardial cells and identified their characteristic expression signatures, comparing them with specific subpopulations found in single cell RNA sequencing datasets. We further characterized the differentiation trajectories of epicardial cells, identifying a clear spatial component on it. All in all, our study provides a novel technique for conducting de novo spatial-temporal analyses in developmental tissue samples and a useful resource for online exploration of cell-type differentiation during heart development at sub-cellular image resolution.
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2.
  • Ke, Rongqin, et al. (författare)
  • In situ sequencing for RNA analysis in preserved tissue and cells
  • 2013
  • Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 10:9, s. 857-860
  • Tidskriftsartikel (refereegranskat)abstract
    • Tissue gene expression profiling is performed on homogenates or on populations of isolated single cells to resolve molecular states of different cell types. In both approaches, histological context is lost. We have developed an in situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved cells and tissue. We demonstrate in situ sequencing of point mutations and multiplexed gene expression profiling in human breast cancer tissue sections.
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