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Spatial Transcriptomics Inc spatial transcriptomics srt

Integration of Single-cell <t>transcriptomics</t> datasets. a Diagram depicting the single-cell transcriptomics dataset utilized. b Highlighted transcriptional states selected from each single-cell transcriptomics dataset, demarcated with dotted lines. c UMAP plot showing 14 distinct integrated clusters labeled 0–13, comprising a total of 222,822 cells. d Quantification of individual cell state contributions to the integrated transcriptional state. e – f Gene expression analysis within each transcriptional state, referencing studies by Yun Chen et al. and Sun Victor et al. . Cluster numbers and gene names are highlighted with the same color code to indicate enrichment. Note: Xenografted-mic term used for Xenografted-microglia

Spatial Transcriptomics Srt, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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spatial transcriptomics srt - by Bioz Stars, 2026-06

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1) Product Images from "Exploring cellular heterogeneity: single-cell and spatial transcriptomics of Alzheimer's disease brains and iPSC-derived microglia"

Article Title: Exploring cellular heterogeneity: single-cell and spatial transcriptomics of Alzheimer's disease brains and iPSC-derived microglia

Journal: Alzheimer's Research & Therapy

doi: 10.1186/s13195-025-01944-y

Integration of Single-cell transcriptomics datasets. a Diagram depicting the single-cell transcriptomics dataset utilized. b Highlighted transcriptional states selected from each single-cell transcriptomics dataset, demarcated with dotted lines. c UMAP plot showing 14 distinct integrated clusters labeled 0–13, comprising a total of 222,822 cells. d Quantification of individual cell state contributions to the integrated transcriptional state. e – f Gene expression analysis within each transcriptional state, referencing studies by Yun Chen et al. and Sun Victor et al. . Cluster numbers and gene names are highlighted with the same color code to indicate enrichment. Note: Xenografted-mic term used for Xenografted-microglia

Figure Legend Snippet: Integration of Single-cell transcriptomics datasets. a Diagram depicting the single-cell transcriptomics dataset utilized. b Highlighted transcriptional states selected from each single-cell transcriptomics dataset, demarcated with dotted lines. c UMAP plot showing 14 distinct integrated clusters labeled 0–13, comprising a total of 222,822 cells. d Quantification of individual cell state contributions to the integrated transcriptional state. e – f Gene expression analysis within each transcriptional state, referencing studies by Yun Chen et al. and Sun Victor et al. . Cluster numbers and gene names are highlighted with the same color code to indicate enrichment. Note: Xenografted-mic term used for Xenografted-microglia

Techniques Used: Single-cell Transcriptomics, Labeling, Gene Expression

$Microglial transcriptional shift in response to AD pathology. a Spatial transcriptomics (SRT) of the Middle Temporal Gyrus (MTG) in Alzheimer's disease (AD), with each section being 10 µm thick. b Visium spots highlighting the top 25% highest probability for Homeostatic, DAM, MHCII, Neuronal Surveillance and Inflammatory-I states. c Heatmap illustrating the fraction of predicted transcriptional states within each cortical layer. d Overview of spatial transcriptomics Aβ localization. Aβ-proximal spots refer to those directly overlapping Aβ plaques, while all others are considered Aβ-distal. e Upper: Quantification of transcriptional states around proximal and distal Aβ spots for Combined II-VI, External II-III, and Internal IV-VI cortical layers. f - j SRT sample from AD frontal cortex from van Olst et al. . f Spatially resolved clusters based on gene expression from van Olst et al. AD sample. g Cortical layers identified based on main layer markers reported in van Olst et al., shown in panel h . The grey matter layers were identified as External (Layers I-III) and Internal (Layers IV-VI). Meninges and white mater were not considered in the analysis. i The Homeostatic and DAM enriched spots identified across the grey matter. j Proportion of Homeostatic and DAM enriched spots in each Internal and External layers. Chi-square significance tests were used to calculate p-values (refer Fig. S9 for other transcriptional states). Note: Xenografted-mic term used for Xenografted-microglia$
Figure Legend Snippet: Microglial transcriptional shift in response to AD pathology. a Spatial transcriptomics (SRT) of the Middle Temporal Gyrus (MTG) in Alzheimer's disease (AD), with each section being 10 µm thick. b Visium spots highlighting the top 25% highest probability for Homeostatic, DAM, MHCII, Neuronal Surveillance and Inflammatory-I states. c Heatmap illustrating the fraction of predicted transcriptional states within each cortical layer. d Overview of spatial transcriptomics Aβ localization. Aβ-proximal spots refer to those directly overlapping Aβ plaques, while all others are considered Aβ-distal. e Upper: Quantification of transcriptional states around proximal and distal Aβ spots for Combined II-VI, External II-III, and Internal IV-VI cortical layers. f - j SRT sample from AD frontal cortex from van Olst et al. . f Spatially resolved clusters based on gene expression from van Olst et al. AD sample. g Cortical layers identified based on main layer markers reported in van Olst et al., shown in panel h . The grey matter layers were identified as External (Layers I-III) and Internal (Layers IV-VI). Meninges and white mater were not considered in the analysis. i The Homeostatic and DAM enriched spots identified across the grey matter. j Proportion of Homeostatic and DAM enriched spots in each Internal and External layers. Chi-square significance tests were used to calculate p-values (refer Fig. S9 for other transcriptional states). Note: Xenografted-mic term used for Xenografted-microglia

Techniques Used: Gene Expression

Spatial distribution of microglial activation across cortical layers in Alzheimer’s disease (AD) brain. a Immunofluorescence (IF) staining of P2RY12 and Aβ on adjacent Sects. (10 µm interval) from the Middle Temporal Gyrus of an AD donor, aligned to 10X Genomics Visium spatial transcriptomics spots (color-coded) across cortical layers II–VI (Chen et al., ANC, 2022) . High-magnification images show nuclei (DAPI, gray), homeostatic microglia (P2RY12, magenta), and Aβ plaques (blue) in external layers II–III (top) and internal layers IV–VI (bottom). b Quantification of IF-stained P2RY12⁺ cells and Aβ⁺ plaques across cortical layers II–III and IV–VI in AD samples. Bar plots display normalized counts for: Upper Left—P2RY12⁺ cells; Upper Right—Aβ⁺ plaques; Lower Left—P2RY12⁺/Aβ⁺ overlap; Lower Right—P2RY12⁺/Aβ⁻ plaques. Counts were normalized to the total number within layers II–VI. c IF co-staining of Aβ (red) and phosphorylated tau (pTAU, green) in frontal cortex sections with AD pathology (Section A). Nuclei stained with DAPI (blue). Adjacent section (Section B) stained for CD68 (red), a marker of activated microglia. d Quantification of CD68⁺ cells across cortical layers in AD frontal cortex. Graph shows distribution of CD68⁺ and CD68⁻ cells in external versus internal layers

Figure Legend Snippet: Spatial distribution of microglial activation across cortical layers in Alzheimer’s disease (AD) brain. a Immunofluorescence (IF) staining of P2RY12 and Aβ on adjacent Sects. (10 µm interval) from the Middle Temporal Gyrus of an AD donor, aligned to 10X Genomics Visium spatial transcriptomics spots (color-coded) across cortical layers II–VI (Chen et al., ANC, 2022) . High-magnification images show nuclei (DAPI, gray), homeostatic microglia (P2RY12, magenta), and Aβ plaques (blue) in external layers II–III (top) and internal layers IV–VI (bottom). b Quantification of IF-stained P2RY12⁺ cells and Aβ⁺ plaques across cortical layers II–III and IV–VI in AD samples. Bar plots display normalized counts for: Upper Left—P2RY12⁺ cells; Upper Right—Aβ⁺ plaques; Lower Left—P2RY12⁺/Aβ⁺ overlap; Lower Right—P2RY12⁺/Aβ⁻ plaques. Counts were normalized to the total number within layers II–VI. c IF co-staining of Aβ (red) and phosphorylated tau (pTAU, green) in frontal cortex sections with AD pathology (Section A). Nuclei stained with DAPI (blue). Adjacent section (Section B) stained for CD68 (red), a marker of activated microglia. d Quantification of CD68⁺ cells across cortical layers in AD frontal cortex. Graph shows distribution of CD68⁺ and CD68⁻ cells in external versus internal layers

Techniques Used: Activation Assay, Immunofluorescence, Staining, Marker

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Journal: Alzheimer's Research & Therapy

Article Title: Exploring cellular heterogeneity: single-cell and spatial transcriptomics of Alzheimer's disease brains and iPSC-derived microglia

doi: 10.1186/s13195-025-01944-y

Figure Lengend Snippet: Integration of Single-cell transcriptomics datasets. a Diagram depicting the single-cell transcriptomics dataset utilized. b Highlighted transcriptional states selected from each single-cell transcriptomics dataset, demarcated with dotted lines. c UMAP plot showing 14 distinct integrated clusters labeled 0–13, comprising a total of 222,822 cells. d Quantification of individual cell state contributions to the integrated transcriptional state. e – f Gene expression analysis within each transcriptional state, referencing studies by Yun Chen et al. and Sun Victor et al. . Cluster numbers and gene names are highlighted with the same color code to indicate enrichment. Note: Xenografted-mic term used for Xenografted-microglia

Article Snippet: Fig. 3 Microglial transcriptional shift in response to AD pathology. a Spatial transcriptomics (SRT) of the Middle Temporal Gyrus (MTG) in Alzheimer's disease (AD), with each section being 10 μm thick. b Visium spots highlighting the top 25% highest probability for Homeostatic, DAM, MHCII, Neuronal Surveillance and Inflammatory-I states. c Heatmap illustrating the fraction of predicted transcriptional states within each cortical layer. d Overview of spatial transcriptomics Aβ localization.

Techniques: Single-cell Transcriptomics, Labeling, Gene Expression

Journal: Alzheimer's Research & Therapy

Article Title: Exploring cellular heterogeneity: single-cell and spatial transcriptomics of Alzheimer's disease brains and iPSC-derived microglia

doi: 10.1186/s13195-025-01944-y

Figure Lengend Snippet: Microglial transcriptional shift in response to AD pathology. a Spatial transcriptomics (SRT) of the Middle Temporal Gyrus (MTG) in Alzheimer's disease (AD), with each section being 10 µm thick. b Visium spots highlighting the top 25% highest probability for Homeostatic, DAM, MHCII, Neuronal Surveillance and Inflammatory-I states. c Heatmap illustrating the fraction of predicted transcriptional states within each cortical layer. d Overview of spatial transcriptomics Aβ localization. Aβ-proximal spots refer to those directly overlapping Aβ plaques, while all others are considered Aβ-distal. e Upper: Quantification of transcriptional states around proximal and distal Aβ spots for Combined II-VI, External II-III, and Internal IV-VI cortical layers. f - j SRT sample from AD frontal cortex from van Olst et al. . f Spatially resolved clusters based on gene expression from van Olst et al. AD sample. g Cortical layers identified based on main layer markers reported in van Olst et al., shown in panel h . The grey matter layers were identified as External (Layers I-III) and Internal (Layers IV-VI). Meninges and white mater were not considered in the analysis. i The Homeostatic and DAM enriched spots identified across the grey matter. j Proportion of Homeostatic and DAM enriched spots in each Internal and External layers. Chi-square significance tests were used to calculate p-values (refer Fig. S9 for other transcriptional states). Note: Xenografted-mic term used for Xenografted-microglia

Techniques: Gene Expression

Journal: Alzheimer's Research & Therapy

Article Title: Exploring cellular heterogeneity: single-cell and spatial transcriptomics of Alzheimer's disease brains and iPSC-derived microglia

doi: 10.1186/s13195-025-01944-y

Figure Lengend Snippet: Spatial distribution of microglial activation across cortical layers in Alzheimer’s disease (AD) brain. a Immunofluorescence (IF) staining of P2RY12 and Aβ on adjacent Sects. (10 µm interval) from the Middle Temporal Gyrus of an AD donor, aligned to 10X Genomics Visium spatial transcriptomics spots (color-coded) across cortical layers II–VI (Chen et al., ANC, 2022) . High-magnification images show nuclei (DAPI, gray), homeostatic microglia (P2RY12, magenta), and Aβ plaques (blue) in external layers II–III (top) and internal layers IV–VI (bottom). b Quantification of IF-stained P2RY12⁺ cells and Aβ⁺ plaques across cortical layers II–III and IV–VI in AD samples. Bar plots display normalized counts for: Upper Left—P2RY12⁺ cells; Upper Right—Aβ⁺ plaques; Lower Left—P2RY12⁺/Aβ⁺ overlap; Lower Right—P2RY12⁺/Aβ⁻ plaques. Counts were normalized to the total number within layers II–VI. c IF co-staining of Aβ (red) and phosphorylated tau (pTAU, green) in frontal cortex sections with AD pathology (Section A). Nuclei stained with DAPI (blue). Adjacent section (Section B) stained for CD68 (red), a marker of activated microglia. d Quantification of CD68⁺ cells across cortical layers in AD frontal cortex. Graph shows distribution of CD68⁺ and CD68⁻ cells in external versus internal layers

Techniques: Activation Assay, Immunofluorescence, Staining, Marker

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