PT - JOURNAL ARTICLE AU - Saiselet, Manuel AU - Rodrigues-Vitória, Joël AU - Tourneur, Adrien AU - Craciun, Ligia AU - Spinette, Alex AU - Larsimont, Denis AU - Andry, Guy AU - Lundeberg, Joakim AU - Maenhaut, Carine AU - Detours, Vincent TI - Transcriptional output, cell types densities and normalization in spatial transcriptomics AID - 10.1101/503870 DP - 2020 Jan 01 TA - bioRxiv PG - 503870 4099 - http://biorxiv.org/content/early/2020/03/27/503870.short 4100 - http://biorxiv.org/content/early/2020/03/27/503870.full AB - Spatial transcriptomics measures mRNA at hundreds of 100 micrometer-diameter spots evenly spread across 6.5×6.9 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.