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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.
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SSA: a novel method for Single-cell and Spatial transcriptomics Alignment
Single-cell RNA sequencing (scRNA-seq) provides expression profiles of individual cells but fails to preserve crucial spatial information. On the other hand, Spatial Transcrip- tomics technologies are able to analyze specific regions within tissue sections, but lack of the capability to examine in single-cell resolution. To overcome these issues, we present Single-cell and Spatial transcriptomics Alignment (SSA), a novel technique that employs an optimal transport algorithm to assign individual cells from a scRNA-seq atlas to their spa- tial locations in actual tissue based on their expression profiles. SSA has demonstrated su- perior performance compared to existing methods SpaOTsc, Tangram, Seurat and DistMap using 10 semi-simulated datasets generated from a high-resolution spatial transcriptomics human breast cancer dataset with 100,064 cells. This advancement provides a refined tool for researchers to delve deeper in understanding of the relationship between cellular spatial organization and gene expression.
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- PAR ID:
- 10583629
- Publisher / Repository:
- EPiC Series in Computing
- Date Published:
- Page Range / eLocation ID:
- 25 to 10
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Conference Paper:
- https://doi.org/10.29007/9cr1
