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Projecting clumped transcriptomes onto single cell atlases to achieve single cell resolution

Nelson Johansen, View ORCID ProfileGerald Quon
doi: https://doi.org/10.1101/2022.04.26.489628
Nelson Johansen
1Graduate Group in Computer Science, University of California, Davis, Davis, CA
2Genome Center, University of California, Davis, Davis, CA
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  • For correspondence: njjohansen@ucdavis.edu gquon@ucdavis.edu
Gerald Quon
1Graduate Group in Computer Science, University of California, Davis, Davis, CA
2Genome Center, University of California, Davis, Davis, CA
3Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA
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  • ORCID record for Gerald Quon
  • For correspondence: njjohansen@ucdavis.edu gquon@ucdavis.edu
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Abstract

Multi-modal single cell RNA assays capture RNA content as well as other data modalities, such as spatial cell position or the electrophysiological properties of cells. Compared to dedicated scRNA-seq assays however, they may unintentionally capture RNA from multiple adjacent cells, exhibit lower RNA sequencing depth compared to scRNA-seq, or lack genome-wide RNA measurements. We present scProjection, a method for mapping individual multi-modal RNA measurements to deeply sequenced scRNA-seq atlases to extract cell type-specific, single cell gene expression profiles. We demonstrate several use cases of scProjection, including the identification of spatial motifs from spatial transcriptome assays, distinguishing RNA contributions from neighboring cells in both spatial and multi-modal single cell assays, and imputing expression measurements of un-measured genes from gene markers. scProjection therefore combines the advantages of both multi-modal and scRNA-seq assays to yield precise multi-modal measurements of single cells.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 28, 2022.
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Projecting clumped transcriptomes onto single cell atlases to achieve single cell resolution
Nelson Johansen, Gerald Quon
bioRxiv 2022.04.26.489628; doi: https://doi.org/10.1101/2022.04.26.489628
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Projecting clumped transcriptomes onto single cell atlases to achieve single cell resolution
Nelson Johansen, Gerald Quon
bioRxiv 2022.04.26.489628; doi: https://doi.org/10.1101/2022.04.26.489628

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