Journal: Cell Reports

Article Title: A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

doi: 10.1016/j.celrep.2025.115240

Figure Lengend Snippet: Single-cell RNA-seq and cluster annotation of wheat root tips (A) UMAP visualization of the three replicates in our scRNA-seq experiment and corresponding atlas metrics. (B) Expression of cell type markers across each cluster. Dot diameter, proportion of cluster cells in a cluster expressing a given gene; color, mean expression across cells in that cluster. (C) Sankey plot showing annotations transferred from Arabidopsis ( Ath ), rice ( Osa ), maize ( Zma ), and single-nuclei wheat (sn Tae ) to our wheat atlas ( Tae ) and corresponding q value. (D and E) Annotated UMAPs with cell type (D) and cell state (E) annotations. Please note that cluster 6 was manually annotated as pericycle based on evidence from STOmics Stereo-seq data and known pericycle marker genes and was therefore marked with an asterisk.

Article Snippet: To experimentally validate the predicted annotations of our soil-grown wheat root meristem atlas obtained from the orthology-based mapping approach, we next optimized and implemented an untargeted spatial transcriptomics (ST) technology called STOmics Stereo-seq , on the same samples as collected for scRNA-seq experiment (see for experimental and analysis details).

Techniques: RNA Sequencing, Expressing, Marker

Journal: Cell Reports

Article Title: A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

doi: 10.1016/j.celrep.2025.115240

Figure Lengend Snippet: scRNA-seq-derived marker gene expression patterns in STOmics Stereo-seq root sections (A) A cross-section of wheat root apical meristem with major cell types annotated. (B–F) UMAP feature plot and STOmics Stereo-seq visualization of marker genes from epidermis (B), cortex (C), phloem (D), xylem (E), and root cap (F).

Article Snippet: To experimentally validate the predicted annotations of our soil-grown wheat root meristem atlas obtained from the orthology-based mapping approach, we next optimized and implemented an untargeted spatial transcriptomics (ST) technology called STOmics Stereo-seq , on the same samples as collected for scRNA-seq experiment (see for experimental and analysis details).

Techniques: Derivative Assay, Marker, Gene Expression

Journal: Cell Reports

Article Title: A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

doi: 10.1016/j.celrep.2025.115240

Figure Lengend Snippet: Tissue-specific markers conserved across Arabidopsis , wheat, rice, and maize or unique to the monocot clade (A) UpSet plot showing the intersections of orthologous groups of xylem markers across Arabidopsis , wheat, rice, and maize. (B–E) Feature plots of a xylem-specific marker across species. (F and G) Spatial expression in STOmics Stereo-seq data (F) and ternary plot showing genome asymmetry information (G) of the same xylem-specific marker in the wheat root meristem. (H) UpSet plot showing the intersections of orthologous groups of cortex markers across Arabidopsis , wheat, rice, and maize. (I–L) Feature plots of a cortex-specific marker unique to monocots. (M and N) Spatial expression in STOmics Stereo-seq data (M) and ternary plot showing genome asymmetry information (N) of the same cortex-specific marker in the wheat root meristem.

Article Snippet: To experimentally validate the predicted annotations of our soil-grown wheat root meristem atlas obtained from the orthology-based mapping approach, we next optimized and implemented an untargeted spatial transcriptomics (ST) technology called STOmics Stereo-seq , on the same samples as collected for scRNA-seq experiment (see for experimental and analysis details).

Techniques: Marker, Expressing

Journal: Cell Reports

Article Title: A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

doi: 10.1016/j.celrep.2025.115240

Figure Lengend Snippet:

Article Snippet: To experimentally validate the predicted annotations of our soil-grown wheat root meristem atlas obtained from the orthology-based mapping approach, we next optimized and implemented an untargeted spatial transcriptomics (ST) technology called STOmics Stereo-seq , on the same samples as collected for scRNA-seq experiment (see for experimental and analysis details).

Techniques: Recombinant, Generated, Gene Expression, Software, Marker