Journal: bioRxiv

Article Title: The DLX/Notch axis is necessary for spatiotemporal regulation of neural cell fate

doi: 10.1101/2025.09.28.679022

Figure Lengend Snippet: (A) Schematic diagram illustrating the sub-anatomical compartments within the embryonic telencephalon, including the ventricular zone (VZ), sub-ventricular zone (SVZ), and mantle zone (MZ). (B) Expression of sub-anatomical markers across sections from E12.5 (left), E13.5 2x coronal, 1x sagittal (middle), E14.5 (right). From left to right column: VZ markers, SVZ markers, and MZ markers. From top to bottom row: telencephalon markers (VZ: Fabp7 , SVZ: St18 , MZ: Dcx ); dorsal telencephalon markers (VZ: Pax6 , SVZ: Eomes , MZ: Tbr1 ), and ventral telencephalon markers (VZ/SVZ: Ascl1, Olig2 , MZ: Nkx2-1 ). (C) Cell type classification following unsupervised clustering and manual annotation. WT sections (top row) and Dlx1/Dlx2 -/- sections (bottom row) for E12.5 (left), E13.5 (2x coronal, 1x sagittal) (middle) and E14.5 (right). v/dNP: ventral/dorsal neural progenitors, v/dIP: ventral/dorsal intermediate progenitors, ThalNeur: thalamic neuron, HypothalNeur: hypothalamic neuron. (D) UMAP plots showing clustering and cell type classification for WT and Dlx1/Dlx2 -/- sections. Legend as shown in (C). (E) Dot plot showing the mean expression of cluster markers in cells in each cluster from (C). Dot sizes denote the fraction of cells expressing the corresponding markers. (F) Bar plot showing the percentage of each cell type in WT and Dlx1/Dlx2 -/- E12.5-E14.5 spatial transcriptomics dataset, summarised based on age and genotype. Legend in (C). (G) Volcano plot showing the differential expression analyses comparing VZ and SVZ of WT vs Dlx1/Dlx2 -/- GE. Thresholds for differentially expressed genes were set at FDR<0.05 and fold change > 1 or < -1. (H) Gene ontology analysis results of all differentially expressed genes in VZ and SVZ of Dlx1/Dlx2 -/- GE.

Article Snippet: Samples were prepared and processed in accordance with manufacturer’s instructions (BGI STOmics Stereo-seq Transcriptomics set for Chip-on-a-slide user manual version B) using the STOmics Transcriptomics kit (STOmics Cat# 111KT114).

Techniques: Expressing, Quantitative Proteomics

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