Extended Data Fig. 3: Quality control of the Visium slides.
From: Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
a, Haematoxylin and eosin staining of the slides in the Visium arrays. Two individuals were selected: proliferative phase A13 and secretory phase A30. Two sections 100 μm apart were analysed. Lumenal epithelium was well preserved in individual A30 and in a small region of A13. b, Scatter plots show the number of genes over the number of counts, where each dot is a feature of the Visium slide. Plots are coloured by the percentage of mitochondrial genes. c, Bar plots showing number of genes on each of the samples. A bimodal distribution corresponding to endometrium and myometrium was shown on each of the cases. d, Visualisation of the number of genes on the Visium slides of sample A30, 152807 slide. A zone with low quality is highlighted in the image. This is probably caused by a technical artifact. No pattern like this was seen in other samples. e, Unbiased clustering of Visium spots defined by Louvain algorithm. f, Estimated amount of mRNA (colour intensity) contributed by each cell population to each spot (colour) shown over the H&E image of the proliferative (A13, 152806 slide) and secretory (A30, 152807 slide) endometrium. Endo = Endometrium; Myo = Myometrium; Epi = Epithelial; uSMC= uterine smooth muscle cell; PV = perivascular.
