Extended Data Fig. 6: Supporting data for the cell atlases of difficult-to-digest and field-grown samples.

a, Expression patterns of cell type marker genes in the rice tiller node cell atlas generated by FXcryo-Cell (Fig. 4a; Supplementary Table 1). The diameter of the dots represents the proportion of cells expressing a specific gene within a given cluster, while the color of the dots indicates the relative expression level of the gene. Dc, dividing cells; Me, meristem-like; Xy, xylem; Xy & Ca, xylem/cambium; Ca, cambium; Ph, phloem; Pe & Pa, pericycle & parenchyma; Ep, epidermis; En & Co, endodermis & cortex; Ex, exodermis; Rc, root cap. b, Expression patterns of cell type marker genes in the wild rice rhizome node cell atlas generated by FXcryo-Cell (Fig. 4b; Supplementary Table 1). The diameter of the dots represents the proportion of cells expressing a specific gene within a given cluster, while the color of the dots indicates the relative expression level of the gene. Dc, dividing cells; Xy, xylem; Te, tracheary elements; Ph & Cc, phloem & companion cells; Co, cortex; En & Ex & Pe, endodermis, exodermis, and pericycle; Ca, cambium; LRP, lateral root primordia; QC, root quiescent center; SMC, shoot meristem like. c, Heatmap showing the top 150 genes from each cluster in the maize crown root cell atlas generated by cryoFX-Cell (Fig. 4d). Cell types are annotated using published maize root marker genes (Supplementary Table 1). The representative genes in each cell type are given on the right. Normalized expression levels are shown. Co, cortex; Ci, cortex initials; En, endodermis; Dc, dividing cells; Pe, pericycle; Ph & Si, phloem & sieve; QC, root quiescent center; Rc, root cap; St, stele (E); St, stele (M); Xy, xylem. d, Joint analysis of the maize root cell atlas generated by cryoFX-Cell (Fig. 4d) and traditional scRNA-seq⁵³. Harmony algorithm was applied to mitigate batch effects. e, Annotation of the integrated maize root tip cell atlas shown in (b), based on the published cell type marker gene (Supplementary Table 1). Different colors represent different cell types.