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dc.contributor.author
Sacher, Fabio
dc.contributor.author
Feregrino, Christian
dc.contributor.author
Tschopp, Patrick
dc.contributor.author
Ewald, Collin Y.
dc.date.accessioned
2021-07-05T15:26:24Z
dc.date.available
2021-06-23T03:12:05Z
dc.date.available
2021-07-05T15:24:25Z
dc.date.available
2021-07-05T15:26:24Z
dc.date.issued
2021-06
dc.identifier.issn
2590-0285
dc.identifier.other
10.1016/j.mbplus.2021.100069
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/490831
dc.identifier.doi
10.3929/ethz-b-000490831
dc.description.abstract
Transcriptomic signatures based on cellular mRNA expression profiles can be used to categorize cell types and states. Yet whether different functional groups of genes perform better or worse in this process remains largely unexplored. Here we test the core matrisome – that is, all genes coding for structural proteins of the extracellular matrix – for its ability to delineate distinct cell types in embryonic single-cell RNA-sequencing (scRNA-seq) data. We show that even though expressed core matrisome genes correspond to less than 2% of an entire cellular transcriptome, their RNA expression levels suffice to recapitulate essential aspects of cell type-specific clustering. Notably, using scRNA-seq data from the embryonic limb, we demonstrate that core matrisome gene expression outperforms random gene subsets of similar sizes and can match and exceed the predictive power of transcription factors. While transcription factor signatures generally perform better in predicting cell types at early stages of chicken and mouse limb development, i.e., when cells are less differentiated, the information content of the core matrisome signature increases in more differentiated cells. Moreover, using cross-species analyses, we show that these cell type-specific signatures are evolutionarily conserved. Our findings suggest that each cell type produces its own unique extracellular matrix, or matreotype, which becomes progressively more refined and cell type-specific as embryonic tissues mature.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Elsevier
en_US
dc.rights.uri
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject
Matrisome
en_US
dc.subject
Matreotype
en_US
dc.subject
Cell type
en_US
dc.subject
scRNA-seq
en_US
dc.subject
Limb development
en_US
dc.title
Extracellular matrix gene expression signatures as cell type and cell state identifiers
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
dc.date.published
2021-05-21
ethz.journal.title
Matrix Biology Plus
ethz.journal.volume
10
en_US
ethz.pages.start
100069
en_US
ethz.size
14 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.grant
The role of extracellular matrix enhancement in promoting healthy aging
en_US
ethz.identifier.scopus
ethz.publication.place
Amsterdam
en_US
ethz.publication.status
published
en_US
ethz.grant.agreementno
163898
ethz.grant.fundername
SNF
ethz.grant.funderDoi
10.13039/501100001711
ethz.grant.program
SNF-Förderungsprofessuren Stufe 2
ethz.date.deposited
2021-06-23T03:12:12Z
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2021-07-05T15:24:33Z
ethz.rosetta.lastUpdated
2021-07-05T15:24:33Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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