Journal: bioRxiv

Article Title: A Pan-Cancer Single-Cell Compendium of Intratumoural Heterogeneity

doi: 10.64898/2026.01.06.693992

Figure Lengend Snippet: a, Hematoxylin and eosin (H&E) staining of breast cancer Patient 2. b-d, spatial maps of Visium HD cells coloured by cell type ( b ), mapped cancer cell state ( c ), and CNV cluster ( d ). e, Heatmap of CNV scores in malignant cells with red and blue indicating gains and losses respectively. Leiden clusters of CNV profiles are shown on the y-axis. f-g, Mean per-gene CNV values along chromosome 11 ( f ) and chromosome 8 ( g ) for each CNV cluster (0 or 1).

Article Snippet: Visium HD data and images were directly downloaded from 10X Genomics’ datasets pages – : https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt , https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression/dataset-human-crc , https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-breast-cancer-fixed-frozen , https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-human-breast-cancer-ff-ultima .

Techniques: Staining

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) Molecular cell type–based neuroanatomy of the goldfish telencephalon. Top: Color scheme shown above for GABAergic and glutamatergic cell types (dendrogram). Center: Eight coronal goldfish sections (goldfish 1), sampled for Visium ST, overlaid with a weighted color map that integrates all goldfish telencephalon cell types. Bottom: Regional parcellation based on color map differences above, each color indicates a different region, and suggested nomenclature annotated by similarity region names according to Northcutt . D , area dorsalis; V , area ventralis; Dc , large-celled subdivision of Dm ; Vsst , ventral Sst; Ppa , nucleus preopticus parvocellularis anterioris; a, anterior; p, posterior; d, dorsal; v, ventral; m, medial; l, lateral. ( B ) Heatmaps of SD (normalized per row) along lateral-medial (left) and dorsal-ventral (right) axes for top axial pattern genes, for goldfish 1 and 2; dots indicate spatial enrichment according to axial color scheme shown above; gray without dot, no enrichment. Right: Summary of axial score per gene (mean of enriched sections). ( C ) Expression of 14 axial-patterned genes across the goldfish telencephalon. Gray, low; red, high.

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Expressing

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) t -SNE visualization of GABAergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type assignment. Right: Expression of three branch-organizing genes. ( B ) All GABA types arranged in dendrogram order (GABA1 to GABA40), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cell type, visualized as pie charts. ( C ) Expression of three branch-organizing genes [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the GABAergic dendrogram for spatial correlation of Visium spots: five scRNA-seq cell types (columns) across eight a.-p. coronal sections (rows).

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Expressing, Marker, Gene Expression

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) t -SNE visualization of glutamatergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type. ( B ) All glutamatergic types, in dendrogram order (GLUT1 to GLUT48), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cluster, visualized as pie charts. ( C ) Expression of two branch-organizing genes, NR2F2 and CNR1, visualized on t -SNE [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the glutamatergic dendrogram for spatial correlation of Visium spots: four scRNA-seq cell types (columns) across eight anterior-posterior coronal sections (rows).

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Marker, Gene Expression, Expressing

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A and B ) t -SNE visualizing comparative species analysis between goldfish and zebrafish telencephalon, with cell types highlighted per species; (A) goldfish and (B) zebrafish. Per cell class, both species’ datasets are integrated (Harmony), followed by DBSCAN clustering. ( C ) Per cell type comparison, scored using KNN classifier. ( D ) Expression of CBLN1, PENK , and SST in the integrated teleostean dataset; dots (cells) colored by species origin. ( E ) Validation of gene expression detected in ST using HCR-FISH. Top row: Corresponding section overviews of genes detected in Visium (left) and HCR (right), where each spot represents a segmented fluorescent cell, colored by normalized expression. Bottom row: Raw fluorescent signal in zoom-ins, as indicated in overview sections.

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Comparison, Expressing, Biomarker Discovery, Gene Expression

Journal: Plants

Article Title: Harnessing Single-Cell and Spatial Transcriptomics for Crop Improvement

doi: 10.3390/plants13243476

Figure Lengend Snippet: Selected publications uncovering potential genes for crop improvement discovered through single-cell and spatial transcriptomics.

Article Snippet: Song et al. employed single-nucleus RNA-seq, 10x Genomics Visium, BMKMANU S1000 from BMKGENE (Beijing, China), and Stereo-seq technologies to generate a comprehensive spatial transcriptomic atlas of tomato callus shoot regeneration [ ].

Techniques: Transformation Assay, Membrane, DNA Methylation Assay, In Situ, Sequencing, Stripping Membranes