Journal: bioRxiv

Article Title: A laser capture microdissection-based method for high-sensitivity transcriptomics from archived FFPE tissue slides with single-cell resolution using LCM-FFPEseq

doi: 10.1101/2025.08.13.669096

Figure Lengend Snippet:

Article Snippet: K562 tissue slides were purchased from AMSBIO (Product Code 3070-0120-5pk) and mounted on PEN membrane 1.0 NF glass slides (ZEISS).

Techniques:

Journal: bioRxiv

Article Title: Brassinosteroids mediate proper coordination of sepal elongation

doi: 10.1101/2025.07.13.664398

Figure Lengend Snippet: Spatial RNAseq further suggests boundary identity, cytokinin signaling, and brassinosteroid signaling are increased in drmy1 . A) Cartoon of a typical transverse section of an ap1cal 35S::AP1-GR cauliflower-like cluster, showing the developing flower buds with initiating sepals on the outer ring . B) Representative brightfield images of transverse sections of WT and drmy1 in the ap1cal 35S::AP1-GR background. n=9 Total WT replicate cauliflower-like clusters, n=22 drmy1 replicate cauliflower-like clusters (See also Figure S3). C) An overlay of which single cell cluster maps with the highest prediction score to each Visium spot on the same tissue shown in panel (B). See figure S3 for a more detailed view of prediction scores from each single cell cluster. D) The proportions of Visium spots grouped by which single cell cluster mapped to each with the highest prediction score (clusters that mapped to <10 spots in either genotype were omitted). For cluster 2 (boundaries), WT = 0.102, drmy1 = 0.232. E-G) Overlays of the percentage of transcripts from cytokinin downregulated genes (E), brassinosteroid downregulated genes (F), and SCT normalized expression of DWF1 , a brassinosteroid biosynthesis gene (G). H) Dotplot showing the differences in expression of genes up and down-regulated by various hormones. For each cell, the percentage of transcripts that come from the set of genes up or downregulated by applications of these hormones according to is calculated, then the mean of all the cells in each cluster is calculated for WT and drmy1 . The size of each dot represents the log of the inverse of the p-value between the mean of the two genotypes with a Bonferroni adjusted threshold of p < 0.00069. The color of each dot represents the percentage increase or decrease of the mean of drmy1 compared to WT. Scale bars 500 μm See also: Figure S3, S4

Article Snippet: To optimize RNA permeabilization, we used the Visium Spatial Tissue Optimization Slide & Reagent Kit, 4 slides (10x Genomics PN-1000193).

Techniques: Expressing