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AIR-SPACE enables the mapping of adaptive immune receptor (AIR) clonotypes and <t>transcriptomics</t> in situ. ( A ) Schematic of the experimental design and methodology, including the generation of long-read (LR) and short-read (SR). ( B ) Spatial mapping of cell types across the LN sections at different time points postinfection. (Scale bar, 500 μm.) ( C ) Spatial mapping of AIR clonotypes across the LN sections, with immunoglobulin (IG) clones shown in blue and T cell receptor (TCR) clones shown in red; outlined with germinal center (GC) regions in LNs from D10PI to D21PI. ( D ) Multiplexed RNA FISH staining for T cell marker Trbc2 (green), B cell marker Ms4a1 (red), and DAPI (blue) across all samples on sister sections. (Scale bar 500 μm.)
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Adventitial fibroblast in human arteries (A) Featureplot of gene score of ECM- and collagen-related genes demonstrating enrichment in AdvFib. (B) Most specific adventitial (Adv) fibroblast marker, PI16 , RNA expression visualized on the RNA-seq UMAP <t>(left),</t> <t>slide-seq</t> spatial transcriptomics map (middle), and RNAscope (right), confirming the spatial identity of PI16-expressing fibroblasts. (C) UMAP visualization of canonical fibroblast marker genes with diffuse expression pattern, including S100A4 , PDGFRA , COL1A1 , and GLI1 , compared to additional new markers SFRP2 and MFAP5. (D) Relative specificity and sensitivities of commonly used and newly identified “fibroblast markers.” (E) Violin plots showing differential expression of key genes implicated in aneurysm FBN1 , TGFBR2 , LOX , FBLN1 , and MFAP5 expressed mostly in AdvFib. See also and .
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Adventitial fibroblast in human arteries (A) Featureplot of gene score of ECM- and collagen-related genes demonstrating enrichment in AdvFib. (B) Most specific adventitial (Adv) fibroblast marker, PI16 , RNA expression visualized on the RNA-seq UMAP <t>(left),</t> <t>slide-seq</t> spatial transcriptomics map (middle), and RNAscope (right), confirming the spatial identity of PI16-expressing fibroblasts. (C) UMAP visualization of canonical fibroblast marker genes with diffuse expression pattern, including S100A4 , PDGFRA , COL1A1 , and GLI1 , compared to additional new markers SFRP2 and MFAP5. (D) Relative specificity and sensitivities of commonly used and newly identified “fibroblast markers.” (E) Violin plots showing differential expression of key genes implicated in aneurysm FBN1 , TGFBR2 , LOX , FBLN1 , and MFAP5 expressed mostly in AdvFib. See also and .
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Adventitial fibroblast in human arteries (A) Featureplot of gene score of ECM- and collagen-related genes demonstrating enrichment in AdvFib. (B) Most specific adventitial (Adv) fibroblast marker, PI16 , RNA expression visualized on the RNA-seq UMAP <t>(left),</t> <t>slide-seq</t> spatial transcriptomics map (middle), and RNAscope (right), confirming the spatial identity of PI16-expressing fibroblasts. (C) UMAP visualization of canonical fibroblast marker genes with diffuse expression pattern, including S100A4 , PDGFRA , COL1A1 , and GLI1 , compared to additional new markers SFRP2 and MFAP5. (D) Relative specificity and sensitivities of commonly used and newly identified “fibroblast markers.” (E) Violin plots showing differential expression of key genes implicated in aneurysm FBN1 , TGFBR2 , LOX , FBLN1 , and MFAP5 expressed mostly in AdvFib. See also and .
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AIR-SPACE enables the mapping of adaptive immune receptor (AIR) clonotypes and transcriptomics in situ. ( A ) Schematic of the experimental design and methodology, including the generation of long-read (LR) and short-read (SR). ( B ) Spatial mapping of cell types across the LN sections at different time points postinfection. (Scale bar, 500 μm.) ( C ) Spatial mapping of AIR clonotypes across the LN sections, with immunoglobulin (IG) clones shown in blue and T cell receptor (TCR) clones shown in red; outlined with germinal center (GC) regions in LNs from D10PI to D21PI. ( D ) Multiplexed RNA FISH staining for T cell marker Trbc2 (green), B cell marker Ms4a1 (red), and DAPI (blue) across all samples on sister sections. (Scale bar 500 μm.)

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: A temporal and spatial atlas of adaptive immune responses in the lymph node following viral infection

doi: 10.1073/pnas.2504742123

Figure Lengend Snippet: AIR-SPACE enables the mapping of adaptive immune receptor (AIR) clonotypes and transcriptomics in situ. ( A ) Schematic of the experimental design and methodology, including the generation of long-read (LR) and short-read (SR). ( B ) Spatial mapping of cell types across the LN sections at different time points postinfection. (Scale bar, 500 μm.) ( C ) Spatial mapping of AIR clonotypes across the LN sections, with immunoglobulin (IG) clones shown in blue and T cell receptor (TCR) clones shown in red; outlined with germinal center (GC) regions in LNs from D10PI to D21PI. ( D ) Multiplexed RNA FISH staining for T cell marker Trbc2 (green), B cell marker Ms4a1 (red), and DAPI (blue) across all samples on sister sections. (Scale bar 500 μm.)

Article Snippet: Slide-seq spatial transcriptomics experiment was performed using the Curio Seeker Kit (Curio Bioscience) according to manufacturer instructions.

Techniques: In Situ, Clone Assay, Staining, Marker

Adventitial fibroblast in human arteries (A) Featureplot of gene score of ECM- and collagen-related genes demonstrating enrichment in AdvFib. (B) Most specific adventitial (Adv) fibroblast marker, PI16 , RNA expression visualized on the RNA-seq UMAP (left), slide-seq spatial transcriptomics map (middle), and RNAscope (right), confirming the spatial identity of PI16-expressing fibroblasts. (C) UMAP visualization of canonical fibroblast marker genes with diffuse expression pattern, including S100A4 , PDGFRA , COL1A1 , and GLI1 , compared to additional new markers SFRP2 and MFAP5. (D) Relative specificity and sensitivities of commonly used and newly identified “fibroblast markers.” (E) Violin plots showing differential expression of key genes implicated in aneurysm FBN1 , TGFBR2 , LOX , FBLN1 , and MFAP5 expressed mostly in AdvFib. See also and .

Journal: Cell Genomics

Article Title: A cell and transcriptome atlas of human arterial vasculature

doi: 10.1016/j.xgen.2025.101034

Figure Lengend Snippet: Adventitial fibroblast in human arteries (A) Featureplot of gene score of ECM- and collagen-related genes demonstrating enrichment in AdvFib. (B) Most specific adventitial (Adv) fibroblast marker, PI16 , RNA expression visualized on the RNA-seq UMAP (left), slide-seq spatial transcriptomics map (middle), and RNAscope (right), confirming the spatial identity of PI16-expressing fibroblasts. (C) UMAP visualization of canonical fibroblast marker genes with diffuse expression pattern, including S100A4 , PDGFRA , COL1A1 , and GLI1 , compared to additional new markers SFRP2 and MFAP5. (D) Relative specificity and sensitivities of commonly used and newly identified “fibroblast markers.” (E) Violin plots showing differential expression of key genes implicated in aneurysm FBN1 , TGFBR2 , LOX , FBLN1 , and MFAP5 expressed mostly in AdvFib. See also and .

Article Snippet: Slide-Seq V2 , Curio , #CB00030 v3.1.

Techniques: Marker, RNA Expression, RNA Sequencing, RNAscope, Expressing, Quantitative Proteomics