Extended Data Fig. 3: Effects of segmentation errors on differential expression in a mouse hypothalamus MERFISH dataset.
From: Impact and correction of segmentation errors in spatial transcriptomics
a, Hypothalamus cell type markers identified in scRNA-seq data. Dot plot of top markers, showing relative gene expression in scRNA-seq data (left) or the corresponding spatial dataset (right). b, Hypothalamus data for one mouse. Cell types are shown as different colored points. Circled regions indicate which contexts were used for comparison in differential expression (red is the ACA region, which is compared to all others). c, Cell-type composition inside and out of the ACA region. Composition is shown as the fraction of all cells in a region coming from cells of a given cell type. d, Differential expression of microglia between ACA and other regions. scRNA-seq marker genes of mature oligodendrocytes cells and inhibitory neurons are shown as red and blue colors, respectively. P-values were calculated from a two-sided Wilcoxon rank-sum test and were FDR adjusted. The marker enrichment p-values were calculated with a GSEA test (two-sided). ACA, anterior commissure area.
