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    10X Genomics mouse brain st data 10x genomics visium
    Utilization of scRank for identifying neuronal subtypes targeted by fluoxetine in MDD (A) Top image displays snRNA-seq dataset of the dorsolateral prefrontal cortex (DLPFC) in Brodmann area 9 (BA9) derived from 17 patients with MDD. The lower image shows a schematic diagram of the mechanism of fluoxetine for MDD. scRNA-seq <t>data</t> for the MDD condition and the fluoxetine target gene were input data for scRank. (B) UMAP visualizations of data with 25 cell types colored based on the predicted rank for drug response. Bar plot shows the scaled perturbation score for each cell type. Ex, excitatory neurons; Inhib, inhibitory neurons; Oligos, oligodendrocytes; Endo, endothelial; Astro, astrocytes; OPC, oligodendrocyte precursor cells. (C) Heatmap of the GRN in excitatory neuron cluster 9 (Ex_9) with 205 MDD risk genes, which were separated into four modules. The top right heatmap represents the subnetwork of modules 2–4 for Ex_9, while the bottom right heatmap represents the network for inhibitory neuron cluster 5 (Inhib_5). Both heatmaps represent the GRN in untreated samples. The graphs to the right of the heatmap provide the network visualizations for module 2 in corresponding cell types, where gene nodes are colored based on their module. (D) Significantly enriched biological processes and pathways for module genes determined using the Metascape web tool. (E) Average module 2 activity for each neuron subtype in MDD. Data are presented as boxplots (minima, 25th percentile; median, 75th percentile; and maxima). The number of data points is 26 for each group. The comparison of the drug-target-related module for Ex_9 between the control group and MDD group is shown on the right, with respect to the averaged edge weight of 26 module 2 genes evaluated via a paired two-sided Wilcoxon test. (F) Averaged log fold change of MDD risk genes between healthy state and disease state. (G) Significantly activated pathways in Ex_9 determined via GSEA of the differentially expressed MDD risk genes. (H and I) Spatial mapping of Ex_9 using CellTrek. The images on the left in both (H) and (I) represent the layer annotation for each spatial spot in <t>mouse</t> anterior <t>brain</t> tissue (H) or human dorsolateral prefrontal cortex tissue (I). The images on the right in (H) and (I) represent the spatial distribution of Ex_9, where red pixels specifically mark the location of these neurons. The deeper layers (layers 5 and 6) are particularly highlighted. The subsequent bar plot shows the relative proportion of cells in each layer.
    Mouse Brain St Data 10x Genomics Visium, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/mouse+brain+st+data+10x+genomics+visium/mouse+brain+sagittal+anterior+dataset+acquired+with+10x+genomics+visium/pmc11228399-392-1-5
    Average 90 stars, based on 1 article reviews
    mouse brain st data 10x genomics visium - by Bioz Stars, 2026-10
    90/100 stars

    Images

    1) Product Images from "scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network"

    Article Title: scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network

    Journal: Cell Reports Medicine

    doi: 10.1016/j.xcrm.2024.101568

    Utilization of scRank for identifying neuronal subtypes targeted by fluoxetine in MDD (A) Top image displays snRNA-seq dataset of the dorsolateral prefrontal cortex (DLPFC) in Brodmann area 9 (BA9) derived from 17 patients with MDD. The lower image shows a schematic diagram of the mechanism of fluoxetine for MDD. scRNA-seq data for the MDD condition and the fluoxetine target gene were input data for scRank. (B) UMAP visualizations of data with 25 cell types colored based on the predicted rank for drug response. Bar plot shows the scaled perturbation score for each cell type. Ex, excitatory neurons; Inhib, inhibitory neurons; Oligos, oligodendrocytes; Endo, endothelial; Astro, astrocytes; OPC, oligodendrocyte precursor cells. (C) Heatmap of the GRN in excitatory neuron cluster 9 (Ex_9) with 205 MDD risk genes, which were separated into four modules. The top right heatmap represents the subnetwork of modules 2–4 for Ex_9, while the bottom right heatmap represents the network for inhibitory neuron cluster 5 (Inhib_5). Both heatmaps represent the GRN in untreated samples. The graphs to the right of the heatmap provide the network visualizations for module 2 in corresponding cell types, where gene nodes are colored based on their module. (D) Significantly enriched biological processes and pathways for module genes determined using the Metascape web tool. (E) Average module 2 activity for each neuron subtype in MDD. Data are presented as boxplots (minima, 25th percentile; median, 75th percentile; and maxima). The number of data points is 26 for each group. The comparison of the drug-target-related module for Ex_9 between the control group and MDD group is shown on the right, with respect to the averaged edge weight of 26 module 2 genes evaluated via a paired two-sided Wilcoxon test. (F) Averaged log fold change of MDD risk genes between healthy state and disease state. (G) Significantly activated pathways in Ex_9 determined via GSEA of the differentially expressed MDD risk genes. (H and I) Spatial mapping of Ex_9 using CellTrek. The images on the left in both (H) and (I) represent the layer annotation for each spatial spot in mouse anterior brain tissue (H) or human dorsolateral prefrontal cortex tissue (I). The images on the right in (H) and (I) represent the spatial distribution of Ex_9, where red pixels specifically mark the location of these neurons. The deeper layers (layers 5 and 6) are particularly highlighted. The subsequent bar plot shows the relative proportion of cells in each layer.
    Figure Legend Snippet: Utilization of scRank for identifying neuronal subtypes targeted by fluoxetine in MDD (A) Top image displays snRNA-seq dataset of the dorsolateral prefrontal cortex (DLPFC) in Brodmann area 9 (BA9) derived from 17 patients with MDD. The lower image shows a schematic diagram of the mechanism of fluoxetine for MDD. scRNA-seq data for the MDD condition and the fluoxetine target gene were input data for scRank. (B) UMAP visualizations of data with 25 cell types colored based on the predicted rank for drug response. Bar plot shows the scaled perturbation score for each cell type. Ex, excitatory neurons; Inhib, inhibitory neurons; Oligos, oligodendrocytes; Endo, endothelial; Astro, astrocytes; OPC, oligodendrocyte precursor cells. (C) Heatmap of the GRN in excitatory neuron cluster 9 (Ex_9) with 205 MDD risk genes, which were separated into four modules. The top right heatmap represents the subnetwork of modules 2–4 for Ex_9, while the bottom right heatmap represents the network for inhibitory neuron cluster 5 (Inhib_5). Both heatmaps represent the GRN in untreated samples. The graphs to the right of the heatmap provide the network visualizations for module 2 in corresponding cell types, where gene nodes are colored based on their module. (D) Significantly enriched biological processes and pathways for module genes determined using the Metascape web tool. (E) Average module 2 activity for each neuron subtype in MDD. Data are presented as boxplots (minima, 25th percentile; median, 75th percentile; and maxima). The number of data points is 26 for each group. The comparison of the drug-target-related module for Ex_9 between the control group and MDD group is shown on the right, with respect to the averaged edge weight of 26 module 2 genes evaluated via a paired two-sided Wilcoxon test. (F) Averaged log fold change of MDD risk genes between healthy state and disease state. (G) Significantly activated pathways in Ex_9 determined via GSEA of the differentially expressed MDD risk genes. (H and I) Spatial mapping of Ex_9 using CellTrek. The images on the left in both (H) and (I) represent the layer annotation for each spatial spot in mouse anterior brain tissue (H) or human dorsolateral prefrontal cortex tissue (I). The images on the right in (H) and (I) represent the spatial distribution of Ex_9, where red pixels specifically mark the location of these neurons. The deeper layers (layers 5 and 6) are particularly highlighted. The subsequent bar plot shows the relative proportion of cells in each layer.

    Techniques Used: Derivative Assay, Inhibition, Activity Assay, Comparison, Control

    Related Articles

    Derivative Assay:

    Article Title: scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network
    Article Snippet: For mouse brain ST data (10X Genomics Visium), we downloaded Seurat objects from ( https://satijalab.org/seurat/articles/spatial_vignette.html ).

    Inhibition:

    Article Title: scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network
    Article Snippet: For mouse brain ST data (10X Genomics Visium), we downloaded Seurat objects from ( https://satijalab.org/seurat/articles/spatial_vignette.html ).

    Activity Assay:

    Article Title: scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network
    Article Snippet: For mouse brain ST data (10X Genomics Visium), we downloaded Seurat objects from ( https://satijalab.org/seurat/articles/spatial_vignette.html ).

    Comparison:

    Article Title: scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network
    Article Snippet: For mouse brain ST data (10X Genomics Visium), we downloaded Seurat objects from ( https://satijalab.org/seurat/articles/spatial_vignette.html ).

    Control:

    Article Title: scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network
    Article Snippet: For mouse brain ST data (10X Genomics Visium), we downloaded Seurat objects from ( https://satijalab.org/seurat/articles/spatial_vignette.html ).



    Similar Products

    mouse brain st data 10x genomics visium  (10X Genomics)
    90
    10X Genomics mouse brain st data 10x genomics visium
    Utilization of scRank for identifying neuronal subtypes targeted by fluoxetine in MDD (A) Top image displays snRNA-seq dataset of the dorsolateral prefrontal cortex (DLPFC) in Brodmann area 9 (BA9) derived from 17 patients with MDD. The lower image shows a schematic diagram of the mechanism of fluoxetine for MDD. scRNA-seq <t>data</t> for the MDD condition and the fluoxetine target gene were input data for scRank. (B) UMAP visualizations of data with 25 cell types colored based on the predicted rank for drug response. Bar plot shows the scaled perturbation score for each cell type. Ex, excitatory neurons; Inhib, inhibitory neurons; Oligos, oligodendrocytes; Endo, endothelial; Astro, astrocytes; OPC, oligodendrocyte precursor cells. (C) Heatmap of the GRN in excitatory neuron cluster 9 (Ex_9) with 205 MDD risk genes, which were separated into four modules. The top right heatmap represents the subnetwork of modules 2–4 for Ex_9, while the bottom right heatmap represents the network for inhibitory neuron cluster 5 (Inhib_5). Both heatmaps represent the GRN in untreated samples. The graphs to the right of the heatmap provide the network visualizations for module 2 in corresponding cell types, where gene nodes are colored based on their module. (D) Significantly enriched biological processes and pathways for module genes determined using the Metascape web tool. (E) Average module 2 activity for each neuron subtype in MDD. Data are presented as boxplots (minima, 25th percentile; median, 75th percentile; and maxima). The number of data points is 26 for each group. The comparison of the drug-target-related module for Ex_9 between the control group and MDD group is shown on the right, with respect to the averaged edge weight of 26 module 2 genes evaluated via a paired two-sided Wilcoxon test. (F) Averaged log fold change of MDD risk genes between healthy state and disease state. (G) Significantly activated pathways in Ex_9 determined via GSEA of the differentially expressed MDD risk genes. (H and I) Spatial mapping of Ex_9 using CellTrek. The images on the left in both (H) and (I) represent the layer annotation for each spatial spot in <t>mouse</t> anterior <t>brain</t> tissue (H) or human dorsolateral prefrontal cortex tissue (I). The images on the right in (H) and (I) represent the spatial distribution of Ex_9, where red pixels specifically mark the location of these neurons. The deeper layers (layers 5 and 6) are particularly highlighted. The subsequent bar plot shows the relative proportion of cells in each layer.
    Mouse Brain St Data 10x Genomics Visium, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/mouse+brain+st+data+10x+genomics+visium/mouse+brain+sagittal+anterior+dataset+acquired+with+10x+genomics+visium/pmc11228399-392-1-5
    Average 90 stars, based on 1 article reviews
    mouse brain st data 10x genomics visium - by Bioz Stars, 2026-10
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    Utilization of scRank for identifying neuronal subtypes targeted by fluoxetine in MDD (A) Top image displays snRNA-seq dataset of the dorsolateral prefrontal cortex (DLPFC) in Brodmann area 9 (BA9) derived from 17 patients with MDD. The lower image shows a schematic diagram of the mechanism of fluoxetine for MDD. scRNA-seq data for the MDD condition and the fluoxetine target gene were input data for scRank. (B) UMAP visualizations of data with 25 cell types colored based on the predicted rank for drug response. Bar plot shows the scaled perturbation score for each cell type. Ex, excitatory neurons; Inhib, inhibitory neurons; Oligos, oligodendrocytes; Endo, endothelial; Astro, astrocytes; OPC, oligodendrocyte precursor cells. (C) Heatmap of the GRN in excitatory neuron cluster 9 (Ex_9) with 205 MDD risk genes, which were separated into four modules. The top right heatmap represents the subnetwork of modules 2–4 for Ex_9, while the bottom right heatmap represents the network for inhibitory neuron cluster 5 (Inhib_5). Both heatmaps represent the GRN in untreated samples. The graphs to the right of the heatmap provide the network visualizations for module 2 in corresponding cell types, where gene nodes are colored based on their module. (D) Significantly enriched biological processes and pathways for module genes determined using the Metascape web tool. (E) Average module 2 activity for each neuron subtype in MDD. Data are presented as boxplots (minima, 25th percentile; median, 75th percentile; and maxima). The number of data points is 26 for each group. The comparison of the drug-target-related module for Ex_9 between the control group and MDD group is shown on the right, with respect to the averaged edge weight of 26 module 2 genes evaluated via a paired two-sided Wilcoxon test. (F) Averaged log fold change of MDD risk genes between healthy state and disease state. (G) Significantly activated pathways in Ex_9 determined via GSEA of the differentially expressed MDD risk genes. (H and I) Spatial mapping of Ex_9 using CellTrek. The images on the left in both (H) and (I) represent the layer annotation for each spatial spot in mouse anterior brain tissue (H) or human dorsolateral prefrontal cortex tissue (I). The images on the right in (H) and (I) represent the spatial distribution of Ex_9, where red pixels specifically mark the location of these neurons. The deeper layers (layers 5 and 6) are particularly highlighted. The subsequent bar plot shows the relative proportion of cells in each layer.

    Journal: Cell Reports Medicine

    Article Title: scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network

    doi: 10.1016/j.xcrm.2024.101568

    Figure Lengend Snippet: Utilization of scRank for identifying neuronal subtypes targeted by fluoxetine in MDD (A) Top image displays snRNA-seq dataset of the dorsolateral prefrontal cortex (DLPFC) in Brodmann area 9 (BA9) derived from 17 patients with MDD. The lower image shows a schematic diagram of the mechanism of fluoxetine for MDD. scRNA-seq data for the MDD condition and the fluoxetine target gene were input data for scRank. (B) UMAP visualizations of data with 25 cell types colored based on the predicted rank for drug response. Bar plot shows the scaled perturbation score for each cell type. Ex, excitatory neurons; Inhib, inhibitory neurons; Oligos, oligodendrocytes; Endo, endothelial; Astro, astrocytes; OPC, oligodendrocyte precursor cells. (C) Heatmap of the GRN in excitatory neuron cluster 9 (Ex_9) with 205 MDD risk genes, which were separated into four modules. The top right heatmap represents the subnetwork of modules 2–4 for Ex_9, while the bottom right heatmap represents the network for inhibitory neuron cluster 5 (Inhib_5). Both heatmaps represent the GRN in untreated samples. The graphs to the right of the heatmap provide the network visualizations for module 2 in corresponding cell types, where gene nodes are colored based on their module. (D) Significantly enriched biological processes and pathways for module genes determined using the Metascape web tool. (E) Average module 2 activity for each neuron subtype in MDD. Data are presented as boxplots (minima, 25th percentile; median, 75th percentile; and maxima). The number of data points is 26 for each group. The comparison of the drug-target-related module for Ex_9 between the control group and MDD group is shown on the right, with respect to the averaged edge weight of 26 module 2 genes evaluated via a paired two-sided Wilcoxon test. (F) Averaged log fold change of MDD risk genes between healthy state and disease state. (G) Significantly activated pathways in Ex_9 determined via GSEA of the differentially expressed MDD risk genes. (H and I) Spatial mapping of Ex_9 using CellTrek. The images on the left in both (H) and (I) represent the layer annotation for each spatial spot in mouse anterior brain tissue (H) or human dorsolateral prefrontal cortex tissue (I). The images on the right in (H) and (I) represent the spatial distribution of Ex_9, where red pixels specifically mark the location of these neurons. The deeper layers (layers 5 and 6) are particularly highlighted. The subsequent bar plot shows the relative proportion of cells in each layer.

    Article Snippet: For mouse brain ST data (10X Genomics Visium), we downloaded Seurat objects from ( https://satijalab.org/seurat/articles/spatial_vignette.html ).

    Techniques: Derivative Assay, Inhibition, Activity Assay, Comparison, Control