The cellular life inside a plant is as vibrant as the blossom. Right, representative cross-section views of the middle part of the samples (transition/elongation zone). Middle, 3D projections (upper) and optical sections (2D, lower) of whole-mount tissue images. The colors of the gene name labels correspond to the colors in the images below. Left, UMAPs showing expression patterns of target genes. e, f, Representative results from the imaging rounds 2 ( e) and 3 ( f). LRC, lateral root cap QC, quiescent center. In the UMAPs, cells are labeled with cell types (left) and regions (right). d, Schematic representation of the root tip and UMAPs displaying root tip scRNA-seq data 18 used in this study. The maximum exposure of 60 z planes of the same position in the tissue is displayed. c, Representative images at different imaging rounds. These steps are repeated until all the DNA barcodes are read. After imaging, bridge probes and fluorescent probes are stripped away, keeping RCPs in place. Each bridge probe is then targeted by one of four fluorescent probes to be imaged. Before each imaging round, four types of bridge probes are hybridized to a set of four DNA barcodes. Amplified DNA barcodes are detected by SBH chemistry through multiple rounds of imaging. During amplification, amine-modified nucleotides are incorporated into the DNA amplicons (RCPs) and stably cross-linked with the cellular protein matrix using a non-reversible amine cross-linker. Barcode-containing DNA probes are circularized by ligation (red star) and amplified in situ by RCA.
a, In fixed whole-mount tissue, target mRNA molecules are hybridized by pairs of DNA probes (SNAIL probes) that harbor mRNA species-specific barcode sequences (pink bars). Whole-mount spatial mapping of root tip cell-type marker genes with PHYTOMap.
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