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De novo spatiotempo...
De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks
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- Marco Salas, Sergio (författare)
- Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för biokemi och biofysik,Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, Solna, Sweden
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- Yuan, Xiao (författare)
- Uppsala universitet,Institutionen för informationsteknologi,Science for Life Laboratory, SciLifeLab
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- Sylven, Christer (författare)
- Karolinska Inst, Dept Med, Stockholm, Sweden
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- Nilsson, Mats (författare)
- Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för biokemi och biofysik,Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, Solna, Sweden
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- Wählby, Carolina, professor, 1974- (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för informationsteknologi
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- Partel, Gabriele, 1988- (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för informationsteknologi,Katholieke Univ Leuven, Lab Multiom Integrat Bioinformat, Dept Human Genet, Leuven, Belgium.;VIB KU Leuven Ctr Brain & Dis Res, Lab Computat Biol, Dept Human Genet, Leuven, Belgium
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(creator_code:org_t)
- 2022-08-12
- 2022
- Engelska.
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Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 18:8
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Matematik -- Matematisk analys (hsv//swe)
- NATURAL SCIENCES -- Mathematics -- Mathematical Analysis (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- Convolutional neural networks
- Cytology
- Image resolution
- Mammals
- Tissue
- Cell data
- Cell types
- Cell typing
- Cellular diversity
- Heart development
- Human heart
- Molecular diversity
- Probabilistics
- Single cells
- Spatio-temporal models
- Cells
- article
- cardiac muscle cell
- cell differentiation
- conception
- convolutional neural network
- fetus heart
- human
- human tissue
- single cell RNA seq
- spatiotemporal analysis
- animal
- genetics
- mammal
- metabolism
- Animals
- Humans
- Myocytes
- Cardiac
- Neural Networks
- Computer
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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