10x visium spatial transcriptomic spots  (Spatial Transcriptomics Inc)

Journal: BMC Bioinformatics

Article Title: SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics

doi: 10.1186/s12859-025-06209-x

Figure Lengend Snippet: SCNT testing on human kidney 10X visium HD dataset. ( A ) Spatial clustering plot based on stPlot showing the distribution of 12 cell clusters across the entire tissue space. ( B ) Spatial distribution of the 12 cell clusters within a sub-region. ( C ) scFeature plot displaying the spatial expression feature of LRP2 within the sub-region

Article Snippet: To demonstrate the functionality of SCNT , we applied it to a 10X Genomics Visium HD dataset of human kidney tissue, following the official tutorial, including dimensionality reduction and clustering.

Techniques: Expressing

Journal: BMC Bioinformatics

Article Title: SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics

doi: 10.1186/s12859-025-06209-x

Figure Lengend Snippet: SCNT testing on human kidney 10X visium HD dataset. ( A ) Spatial clustering plot based on stPlot showing the distribution of 12 cell clusters across the entire tissue space. ( B ) Spatial distribution of the 12 cell clusters within a sub-region. ( C ) scFeature plot displaying the spatial expression feature of LRP2 within the sub-region

Article Snippet: SCNT currently supports SC data generated from all major platforms, as well as ST data from 10X Genomics Visium and Visium HD.

Techniques: Expressing

Journal: bioRxiv

Article Title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

doi: 10.1101/2025.07.14.664821

Figure Lengend Snippet: ( A ) dACC (blue) and dlPFC (pink) regions outlined in midsagittal (dACC) and lateral (dlPFC) brain views, as well as in coronal hemislabs. dACC tissue (blue) used here was sourced from the same ten neurotypical control donors previously profiled for dlPFC (pink) to facilitate within-donor comparisons of dACC agranular cortex versus dlPFC granular cortex (bottom). ( B ) Fresh-frozen coronal brain slab from donor Br3942 taken at the level of the anterior striatum overlaid with the outline of major landmarks from the Atlas of the Human Brain . Three Brodmann areas (BA) 33, 24, and 32 corresponding to the dACC are highlighted in yellow (top left). H&E staining of tissue cryosections confirmed inclusion of dACC on the tissue block (top right). Following anatomical validation, cryosections from 10 neurotypical control donors were collected for Visium and Chromium assays (10x Genomics) from the same block for each donor (bottom).

Article Snippet: Scored 10 μm sections from each of the 10 dACC tissue blocks , were collected onto a 10x Visium Gene Expression slide, and processed according to manufacturer’s instructions (protocol number CG000239, Rev G, 10X Genomics) as previously described ( ; ).

Techniques: Control, Staining, Blocking Assay, Biomarker Discovery

Journal: bioRxiv

Article Title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

doi: 10.1101/2025.07.14.664821

Figure Lengend Snippet: ( A ) Fresh-frozen coronal brain slabs from the n=10 neurotypical control donors. Dashed boxes indicate the location of the dissected blocks in ( C ). Inset depicts a midsagittal view of the brain with five subdivisions of the cingulate cortex (red - subgenual region; orange - pregenual region; blue - anterior-dorsal ACC or anterior MCC; purple - posterior-dorsal ACC or posterior MCC; lavender - posterior cingulate cortex). Dashed line across the midsagittal schematic indicates the level of the coronal slab. Neuroanatomical orientation is indicated by arrows: D - dorsal; L - lateral; M - medial. ( B ) Brain atlas schematic corresponding to the level of the coronal cut of the brain slab in ( A ). Brodmann areas (BAs), BA33, BA24, and BA32, which make up the cingulate cortex, are indicated. CC - corpus callosum. Dashed boxes indicate the location of the dissected blocks in ( C ). ( C ) Quality control experiment summary for each dissected brain block. RNAScope experiments with probes marking MBP (white matter), SLC17A7 (excitatory neurons), and/or RELN (Layer 1), are presented in green, pink, and white, respectively. Images of H&E or unprocessed brain blocks with all relevant structures of the block are indicated: BA24, BA33, CC - corpus callosum. Dashed boxes indicate the area of tissue placed on the Visium array in ( D ). ( D ). Sections from each donor, as placed on Visium arrays, rotated to match the orientation of each slab. BAs are indicated; CC - corpus callosum. Neuroanatomical orientation is indicated by arrows: D - dorsal; L - lateral; M - medial.

Article Snippet: Scored 10 μm sections from each of the 10 dACC tissue blocks , were collected onto a 10x Visium Gene Expression slide, and processed according to manufacturer’s instructions (protocol number CG000239, Rev G, 10X Genomics) as previously described ( ; ).

Techniques: Control, Blocking Assay, RNAscope

Journal: bioRxiv

Article Title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

doi: 10.1101/2025.07.14.664821

Figure Lengend Snippet: ( A ) Histological image of Visium capture area from donor Br8667 (sample ID: V12Y31-080_B1). ( B ) Spot plot of Visium capture area from donor Br8667 (sample ID: V12Y31-080_B1) with spots colored by histology-driven domains, which were annotated as Layer 1 (L1), L2/3, L5, L6, white matter (WM), and corpus callosum (CC). ( C ) Spot plot of Visium capture area from donor Br8667 (sample ID: V12Y31-080_B1) with spots colored by the 7 spatial domains annotated from the k =9 PRECAST clusters, which were annotated as L1, L2, L3, L5, L6a, L6b, and WM. ( D ) spatialLIBD spatial registration heatmap displays Pearson’s correlation values between the top 100 marker genes in each data-driven spatial domain ( y -axis) and in each histology-driven manually annotated spatial domain ( x -axis). ( E ) Boxplots of ADCYAP1 log 2 (counts per million + 1) expression (computed manually) ( y -axis) for each spatial domain ( x -axis) in the pseudobulked dACC SRT data. Color represents the spatial domain. escheR spot plot of dACC Visium capture area from donor Br6432 (sample ID: V12N28-331_B1) with spots colored by the dACC spatial domains. Fill represents ADCYAP1 log 2 -normalized expression per spot. ( F ) Boxplots of ADCYAP1 log 2 (counts per million + 1) expression (computed manually) ( y -axis) for each spatial domain ( x -axis) in the pseudobulked dlPFC SRT data. Color represents the spatial domain. Spot plot of dlPFC Visium capture area from donor Br6432 (sample ID: Br6432_ant) with spots colored by the dlPFC spatial domains. Fill represents ADCYAP1 log 2 -normalized expression per spot. ( G ) Same as ( E ), but for RORB expression. ( H ) Same as ( F ), but for RORB expression. ( I ) Same as ( E ), but for PCP4 expression. ( J ) Same as ( F ), but for PCP4 expression. ( K ) Multiplex RNAScope single molecule fluorescence in situ hybridization (smFISH) in dACC of donor Br6432 for ADCYAP1 (magenta) , RORB (green) , PCP4 (red), and merged all channels with DAPI (blue). Approximate cortical layer boundaries are indicated by dashed lines. Scale bar 500 µm. ( L ) Same as ( K ), but for dlPFC.

Article Snippet: Scored 10 μm sections from each of the 10 dACC tissue blocks , were collected onto a 10x Visium Gene Expression slide, and processed according to manufacturer’s instructions (protocol number CG000239, Rev G, 10X Genomics) as previously described ( ; ).

Techniques: Marker, Expressing, Multiplex Assay, RNAscope, Fluorescence, In Situ Hybridization

Journal: bioRxiv

Article Title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

doi: 10.1101/2025.07.14.664821

Figure Lengend Snippet: Each row shows information for one gene, in order, RELN, LAMP5, NR4A2, MOBP. Each column displays a similar style of plot. First column ( A, E, I, M ): The y -axis displays log 2 (counts per million + 1) expression (computed manually) for each spatial domain ( x -axis) in the pseudobulked dACC SRT data. Color represents the spatial domain. Second column ( B, F, J, N ): escheR spot plot of dACC Visium capture area from donor Br6432 (sample ID: V12N28-331_B1) with spots colored by the dACC spatial domains. Fill represents log 2 -normalized expression per spot. Third column ( C, G, K, O ): The y -axis displays log 2 (counts per million + 1) expression (computed manually) for each spatial domain ( x -axis) in the pseudobulked dlPFC SRT data. Color represents the spatial domain. Fourth column ( D, H, L, P ): Spot plot of dlPFC Visium capture area from donor Br6432 (sample ID: Br6432_ant) with spots colored by the dlPFC spatial domains. Fill represents log 2 -normalized expression per spot.

Article Snippet: Scored 10 μm sections from each of the 10 dACC tissue blocks , were collected onto a 10x Visium Gene Expression slide, and processed according to manufacturer’s instructions (protocol number CG000239, Rev G, 10X Genomics) as previously described ( ; ).

Techniques: Expressing

Journal: bioRxiv

Article Title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

doi: 10.1101/2025.07.14.664821

Figure Lengend Snippet: ( A ) Uniform manifold approximation and projection (UMAP) representation of the snRNA-seq dataset. Each point is an individual nucleus colored by its Azimuth reference cell type. Astro: Astrocyte; Endo: Endothelial cell; L2_3_IT: Layer 2-3 glutamatergic neuron, intratelencephalon-projecting; L5_ET: Layer 5 glutamatergic neuron, extratelencephalon-projecting; L5 IT: Layer 5 glutamatergic neuron, intratelencephalon-projecting; L5_6_NP: Layer 5-6 glutamatergic neuron, near-projecting; L6_CT: Layer 6 glutamatergic neuron, corticothalamic-projecting; L6_IT: Layer 6 glutamatergic neuron, intratelencephalon-projecting; L6_IT_Car3: Layer 6 Car3+ glutamatergic neuron, intratelencephalon-projecting; L6b: Layer 6b glutamatergic neuron; Lamp5: Lamp5+ GABAergic neuron; MicroPVM: microglia / perivascular macrophage; Oligo: oligodendrocyte; OPC: oligodendrocyte precursor cell; Pvalb: Pvalb+ GABAergic neuron; Sncg: Sncg+ GABAergic neuron; Sst: Sst+ GABAergic neuron; Vip: Vip+ GABAergic neuron; VLMC: Vip+ GABAergic neuron. ( B ) Heatmap showing two selected marker gene log 2 -normalized expression averaged by cell type and scaled per gene (columns) across the layer-specific cell types (rows): L2/3 IT, L5 ET, L5 IT, L5/6 NP, L6 CT, L6 IT, L6 IT Car3, and L6b. Grouping and color across the top indicates the cell types. ( C ) spatialLIBD spatial registration heatmap displays Pearson’s correlation values between the top 100 marker genes in each SRT data-driven spatial domain and in each snRNA-seq cell type. The x -axis displays the snRNA-seq cell types described in ( A ). The y -axis displays the data-driven domains: L1, L2, L3, L5, L6a, L6b, and white matter (WM). ( D ) Dot plot showing the top NMF pattern ( x -axis) selected for each snRNA-seq cell type ( y -axis). Dot size represents the proportion of nuclei with nonzero weight for each NMF pattern across each cell type. Dot color represents the aggregated nuclei-level weights for each NMF pattern across each cell type. ( E ) Heatmap showing 5 selected marker gene loadings scaled by total gene loadings (columns) across the layer-associated NMF patterns (rows): L2/3 IT, L5 ET, L5 IT, L5/6 NP, L6 CT, L6 IT, L6 IT Car3, and L6b. Grouping across the top indicates the NMF patterns and the color represents the cell type each pattern is associated with. ( F ) escheR spot plots of dACC Visium capture area from donor Br8667 (sample ID: V12Y31-080_B1) with spots colored by the dACC spatial domains. Grey scale fill represents weights of distinct cell type-specific NMF gene expression patterns learned from the snRNA-seq dataset and projected into the SRT data using transfer learning.

Article Snippet: Scored 10 μm sections from each of the 10 dACC tissue blocks , were collected onto a 10x Visium Gene Expression slide, and processed according to manufacturer’s instructions (protocol number CG000239, Rev G, 10X Genomics) as previously described ( ; ).

Techniques: Marker, Expressing, Gene Expression

Journal: bioRxiv

Article Title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

doi: 10.1101/2025.07.14.664821

Figure Lengend Snippet: ( A ) Cytoarchitecture of dACC agranular cortex and dlPFC granular cortex at laminar resolution highlighting the relative location of VENs in Layer 5 ET. This cell type was captured by NMF61. ( B ) UMAP plot from shows cell types from the dACC snRNA-seq data. The L5 NMF patterns derived from these data are projected into the SRT data shown in . ( C ) First spot plot is the same as . The second spot plot shows Visium capture area from dlPFC donor Br8667 (sample ID: Br8667_mid) with spots colored by the 7 spatial domains annotated from the previous dlPFC study . ( D ) TOP ROW: escheR spot plot of dACC Visium capture area from donor Br8667 (sample ID: V12Y31-080_B1) with spots colored by the dACC spatial domains. Spot plot of dlPFC Visium capture area from donor Br8667 (sample ID: Br8667_mid) with spots colored by the dlPFC spatial domains. Fill represents NMF38 projected into the dlPFC and dACC SRT datasets. BOTTOM ROW: Spot plot of dACC Visium capture area from donor Br8667 (sample ID: V12Y31-080_B1) with spots colored by the dACC spatial domains. Spot plot of dlPFC Visium capture area from donor Br8667 (sample ID: Br8667_mid) with spots colored by the dlPFC spatial domains. Fill represents NMF61 projected into the dlPFC and dACC SRT datasets. ( E ) FIRST COLUMN: Boxplots comparing NMF38 and NMF61 between dACC and dlPFC Layer 5 spatial domain. The top boxplots are made up of sample averages of the fraction of nonzero NMF38 spots in the dACC SRT Layer 5 and the dlPFC SRT Layer 5. The bottom boxplots are made up of sample averages of the fraction of nonzero NMF61 spots in the dACC SRT Layer 5 and the dlPFC SRT Layer 5. SECOND COLUMN: Boxplots comparing NMF38 and NMF61 between dACC and dlPFC Layer 5 cell types. The top boxplots show sample averages of NMF38 weights within the dACC snRNA-seq L5 IT cell type and the dlPFC snRNA-seq Excitatory L5 cell type. The bottom boxplots show sample averages of NMF61 weights within the dACC snRNA-seq L5 ET cell type and the dlPFC snRNA-seq Excitatory L5 cell type. ( F ) Left: Differential expression volcano plot compares pseudobulked snRNA-seq cell types L5 IT and L5 ET. Right: Differential expression volcano plot compares pseudobulked spots with nonzero NMF38 and NMF61 projections in the dACC SRT data. Known VEN markers ( VAT1L , SULF2 , HAPLN4 , FEZF2 , and GABRQ ) are highlighted in both volcano plots as upregulated in L5 ET or NMF61. ( G ) Multiplex RNAScope single molecule fluorescence in situ hybridization (smFISH) in dACC (top box) and dlPFC (bottom box) for SULF2, POU3F1, GABRQ, and merged of all. Heatmaps: Top heatmap displays the average proportion of cells called as expressing one gene (row label) that are also called as expressing another gene (column label), averaged across the three dACC samples. Bottom heatmap is similar, except averaged across the two dlPFC samples. Boxplots: Top boxplots display the proportion of cells ( y -axis) from Layer 5 that were called as expressing both POU3F1 and GABRQ ( x -axis). Bottom boxplots display Spearman’s correlation values ( y -axis) for POU3F1 and GABRQ expression ( x -axis). Color indicates the region of the sample, either dACC or dlPFC. Shape indicates the brain donor of the sample, either Br6432 or Br8325. Scale bar 30 µm. ( H ) Dot plot of cortical layer-specific NMF patterns (columns) in the dACC human snRNA-seq dataset corresponding to the nuclei collection source (rows) for the mouse retroviral tracing dataset. Dot size represents the proportion of nuclei with nonzero weight for each NMF pattern across each cell type. Dot color represents the aggregated nuclei-level weights for each NMF pattern across each cell type. ( I ) Dot plot of mouse retroviral tracing using projection of cortical layer-specific NMF patterns (columns). Rows represent axonal projection target regions from the retroviral tracing experiments: AI: agranular insular cortex, AMY: amygdala, AUDp: primary auditory cortex, ENT: entorhinal cortex, MOp: primary motor cortex, P: pons, PFC: prefrontal cortex, PIR: piriform area, PTLp: posterior parietal cortex, RSP: retrosplenial cortex, SC: superior colliculus, SSp: primary somatosensory cortex, STR: striatum, TH: thalamus, VISp: primary visual cortex, and VTA: ventral tegmental area. Dot size represents the proportion of nuclei with nonzero weight for each NMF pattern across each cell type. Dot color represents the aggregated nuclei-level weights for each NMF pattern across each cell type.

Article Snippet: Scored 10 μm sections from each of the 10 dACC tissue blocks , were collected onto a 10x Visium Gene Expression slide, and processed according to manufacturer’s instructions (protocol number CG000239, Rev G, 10X Genomics) as previously described ( ; ).

Techniques: Derivative Assay, Quantitative Proteomics, Multiplex Assay, RNAscope, Fluorescence, In Situ Hybridization, Expressing, Retroviral

Journal: bioRxiv

Article Title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

doi: 10.1101/2025.07.14.664821

Figure Lengend Snippet: ( A ) Pseudobulked sample-level comparison: spatialLIBD spatial registration heatmap displays Pearson’s correlation values between the top 100 marker genes in each dlPFC SRT spatial domain and in each dACC SRT spatial domain. The x -axis displays dlPFC spatial domains: L1, L2, L3, L4, L5, L6, and white matter (WM). The y -axis displays the dACC spatial domains described in . The black “X” represents high confidence. ( B ) Pseudobulked gene-level comparison: the heatmap displays the number of DEGs between each spatial domain in dACC and dlPFC, scaled by the proportion of DEGs across each dACC spatial domain. The x -axis displays dlPFC spatial domains: L1, L2, L3, L4, L 5, L6, and WM. The y -axis displays the dACC spatial domains described in . ( C ) TOP ROW: Spot plot of dACC Visium capture area from donor Br8667 (sample ID: V12Y31-080_B1) with spots colored by the dACC spatial domains. Spot plot of dlPFC Visium capture area from donor Br8667 (sample ID: Br8667_mid) with spots colored by the dlPFC spatial domains. Fill represents NMF15 projected into the dlPFC and dACC SRT datasets. BOTTOM ROW: Spot plot of dACC Visium capture area from donor Br8667 (sample ID: V12Y31-080_B1) with spots colored by the dACC spatial domains. Spot plot of dlPFC Visium capture area from donor Br8667 (sample ID: Br8667_mid) with spots colored by the dlPFC spatial domains. Fill represents NMF35 projected into the dlPFC and dACC SRT datasets. ( D ) Each scatterplot shows a comparison of the log fold-change (logFC) between one spatial domain in dACC and dlPFC SRT spatial domains. Each point is a gene. The x -axis of the first plot shows the logFC from enrichment model pseudobulked DE testing comparing L2 to all other spatial domains for dACC. The y -axis of the first plot shows the logFC from enrichment model pseudobulked DE testing comparing L2 to all other spatial domains for dlPFC. The second plot compares L5 in the dACC to L5 in the dlPFC. The third plot compares L6a in the dACC to L6 in the dlPFC. The fourth plot compares L6b in the dACC to L6 in the dlPFC. The colors highlight genes that are classified as either dACC enriched (red), dlPFC enriched (blue), or both (purple), where the threshold is a logFC greater than 1.25. The number of genes in each category is as follows: L2 dACC vs. L2 dlPFC: 117 dACC enriched and 24 dlPFC and dACC enriched; L5 dACC vs. L5 dlPFC: 80 dACC enriched, 9 dlPFC enriched, 18 dlPFC and dACC enriched; L6a dACC vs. L6 dlPFC: 42 dACC enriched, 2 dlPFC enriched, 19 dlPFC and dACC enriched; L6b dACC vs. Lb dlPFC: 191 dACC enriched, 11 dlPFC enriched, 10 dlPFC and dACC enriched. ( E ) Boxplots comparing gene expression of DRD5, KCTD8, and CPLX3 across pseudobulked spatial domains from dACC SRT data and dlPFC SRT data. The y -axis displays log 2 (counts per million + 1) expression (computed manually) for each spatial domain ( x -axis), for dACC (top row) and dlPFC (bottom row). Color represents spatial domains for each dataset. ( F ) Multiplex RNAScope single molecule fluorescence in situ hybridization (smFISH) in dACC (top row) and dlPFC (bottom row) for DRD5 (magenta) , KCTD8 (yellow) , CPLX3 (green), and merged of all channels with DAPI (blue). Approximate cortical layer boundaries are indicated by dashed lines. Scale bars 500 µm.

Article Snippet: Scored 10 μm sections from each of the 10 dACC tissue blocks , were collected onto a 10x Visium Gene Expression slide, and processed according to manufacturer’s instructions (protocol number CG000239, Rev G, 10X Genomics) as previously described ( ; ).

Techniques: Comparison, Marker, Gene Expression, Expressing, Multiplex Assay, RNAscope, Fluorescence, In Situ Hybridization

Journal: bioRxiv

Article Title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain

doi: 10.1101/2025.07.14.664821

Figure Lengend Snippet: Each row shows information for one gene, in order, RSPO2, CRHBP, ADRA2A. Each column displays a similar style of plot. First column ( A, E, I ): The y -axis displays log 2 (counts per million + 1) expression (computed manually) for each spatial domain ( x -axis) in the pseudobulked dACC SRT data. Color represents the spatial domain. Second column ( B, F, J ): escheR spot plot of dACC Visium capture area from donor Br6432 (sample ID: V12N28-331_B1) with spots colored by the dACC spatial domains. Fill represents log 2 -normalized expression per spot. Third column ( C, G, K ): The y -axis displays log 2 (counts per million + 1) (computed manually) expression for each spatial domain ( x -axis) in the pseudobulked dlPFC SRT data. Color represents the spatial domain. Fourth column ( D, H, L ): Spot plot of dlPFC Visium capture area from donor Br6432 (sample ID: Br6432_ant) with spots colored by the dlPFC spatial domains. Fill represents log 2 -normalized expression per spot.

Article Snippet: Scored 10 μm sections from each of the 10 dACC tissue blocks , were collected onto a 10x Visium Gene Expression slide, and processed according to manufacturer’s instructions (protocol number CG000239, Rev G, 10X Genomics) as previously described ( ; ).

Techniques: Expressing