Fig. 2: Spatial transcriptomics enables simultaneous capture of M. truncatula and R. irregularis transcripts.
From: Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis
a, M. truncatula root tissue is flash frozen to create 16 µm thick cryosections, each containing numerous root cross-sections. Cryosections are fixed to capture areas, each of which is equipped with ~5,000 spatially barcoded voxels at a resolution of 55 µm. b, Side-by-side images of brightfield tissue image and underlying spatial capture voxels, with a close-up view of a single root cross-section within the capture area (one representative capture area out of nine mycorrhizal capture areas was analysed) highlighting voxel size in relation to the tissue. c, Capture area containing cross-sections from M. truncatula roots infected with R. irregularis at 28 dpi (one representative capture area out of nine mycorrhizal capture areas analysed). Image of root cross-sections within capture area (i). UMI count (ii) and feature count (iii) overlaid onto spots underlying tissue. Expression pattern of all R. irregularis transcripts captured (scale, log2 of UMI counts) (iv). Expression pattern of the arbuscule marker gene post-imputation (v), MtPT4, exhibiting overlap in spots with the highest expression of fungal transcripts (scale, log2 of UMI counts). Visualization done in Loupe Browser.
