Journal of Molecular Cell BiologyGenomicsPeer-reviewed journal article
Transcriptional output, cell types densities and normalization in spatial transcriptomics
Manuel Saiselet, Joel Rodrigues VitóriaiD, Adrien TourneuriD, Ligia CraciuniD, Alex SpinetteiD, Denis LarsimontiD, Guy AndryiD, Joakim LundebergiD, Carine Maenhaut, Vincent DetoursiD
Abstract
Spatial transcriptomics measures mRNA at hundreds of 100 micrometer-diameter spots evenly spread across 6.5x6.9 mm2 histological slices. Gene expression within each spot is commonly normalized by total read counts. However we show that the transcriptional output of individual spots reflects the number of cells they contain, hence total read counts per spot reflect relevant biology. Although per-spot read-count normalization reveals important enrichment trends, it may heavily distort cell-type-related absolute local expression and conceal important biological information.
- Citations
- 65
- FWCI
- 2.51
- Field percentile
- top 9%
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