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xenium prime 5k spatial transcriptomics  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc xenium prime 5k spatial transcriptomics
    (A, C) Total and (B, D) virus-specific ASCs were quantified in the liver at week 4 post-infection for (A, B) RHV and (C, D) LCMV clone 13 infection with (E, F) representative ELISpot images showing (A, B) representative and (C, D) pooled data from (A-D) n = 2 independent experiments. Mice were either untreated (WT) or splenectomized and treated with FTY720 prior to infection with treatment being maintained throughout (splX + FTY720 [D -1]). Virus localization was determined by viral transcript density for individual portal and central zones at week 1 post-infection during (G) RHV and (H) LCMV clone 13 infection from n = 10 portal and n = 10 central zone selections from a Xenium 5 K spatial <t>transcriptomics</t> run of n = 1 mouse liver per group. Transcript density of genes associated with oxidative phosphorylation usage were quantified in (I) portal zone hepatocyte regions and (J) immature lymphocytic clusters at week 1 post-infection. Following (K) upstream staining, (L-O) individual transcript localization was determined in the liver at week 1 post-infection. (A-D, G-J) Mean + SEM. (A-D, G-J) Two-tailed, unpaired t-tests were performed. (A) p = 0.9168, (B) p = 0.1987, (C) p = 0.0008, (D) p < 0.0001, (G) p = 0.0261, (H) p = 0.0282. Statistical significance was denoted as *=(p ≤ 0.05), **=(p ≤ 0.01), ***=(p ≤ 0.001), and ****=(p ≤ 0.0001).
    Xenium Prime 5k Spatial Transcriptomics, 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
    https://www.bioz.com/product/xenium+spatial+transcriptome+analysis/5k+prime+xenium/pmc12823446-119-26-29
    Average 86 stars, based on 1 article reviews
    xenium prime 5k spatial transcriptomics - by Bioz Stars, 2026-10
    86/100 stars

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    1) Product Images from "iHALT unlocks liver functionality as a surrogate secondary lymphoid organ"

    Article Title: iHALT unlocks liver functionality as a surrogate secondary lymphoid organ

    Journal: Nature

    doi: 10.1038/s41586-025-09803-4

    (A, C) Total and (B, D) virus-specific ASCs were quantified in the liver at week 4 post-infection for (A, B) RHV and (C, D) LCMV clone 13 infection with (E, F) representative ELISpot images showing (A, B) representative and (C, D) pooled data from (A-D) n = 2 independent experiments. Mice were either untreated (WT) or splenectomized and treated with FTY720 prior to infection with treatment being maintained throughout (splX + FTY720 [D -1]). Virus localization was determined by viral transcript density for individual portal and central zones at week 1 post-infection during (G) RHV and (H) LCMV clone 13 infection from n = 10 portal and n = 10 central zone selections from a Xenium 5 K spatial transcriptomics run of n = 1 mouse liver per group. Transcript density of genes associated with oxidative phosphorylation usage were quantified in (I) portal zone hepatocyte regions and (J) immature lymphocytic clusters at week 1 post-infection. Following (K) upstream staining, (L-O) individual transcript localization was determined in the liver at week 1 post-infection. (A-D, G-J) Mean + SEM. (A-D, G-J) Two-tailed, unpaired t-tests were performed. (A) p = 0.9168, (B) p = 0.1987, (C) p = 0.0008, (D) p < 0.0001, (G) p = 0.0261, (H) p = 0.0282. Statistical significance was denoted as *=(p ≤ 0.05), **=(p ≤ 0.01), ***=(p ≤ 0.001), and ****=(p ≤ 0.0001).
    Figure Legend Snippet: (A, C) Total and (B, D) virus-specific ASCs were quantified in the liver at week 4 post-infection for (A, B) RHV and (C, D) LCMV clone 13 infection with (E, F) representative ELISpot images showing (A, B) representative and (C, D) pooled data from (A-D) n = 2 independent experiments. Mice were either untreated (WT) or splenectomized and treated with FTY720 prior to infection with treatment being maintained throughout (splX + FTY720 [D -1]). Virus localization was determined by viral transcript density for individual portal and central zones at week 1 post-infection during (G) RHV and (H) LCMV clone 13 infection from n = 10 portal and n = 10 central zone selections from a Xenium 5 K spatial transcriptomics run of n = 1 mouse liver per group. Transcript density of genes associated with oxidative phosphorylation usage were quantified in (I) portal zone hepatocyte regions and (J) immature lymphocytic clusters at week 1 post-infection. Following (K) upstream staining, (L-O) individual transcript localization was determined in the liver at week 1 post-infection. (A-D, G-J) Mean + SEM. (A-D, G-J) Two-tailed, unpaired t-tests were performed. (A) p = 0.9168, (B) p = 0.1987, (C) p = 0.0008, (D) p < 0.0001, (G) p = 0.0261, (H) p = 0.0282. Statistical significance was denoted as *=(p ≤ 0.05), **=(p ≤ 0.01), ***=(p ≤ 0.001), and ****=(p ≤ 0.0001).

    Techniques Used: Virus, Infection, Enzyme-linked Immunospot, Phospho-proteomics, Staining, Two Tailed Test

    a – c , H&E staining of formalin-fixed, paraffin-embedded (FFPE) spleen ( a ) and mesenteric lymph node ( b ) sections at 4 weeks post-LCMV infection and a liver section at 4 weeks post-RHV infection ( c ). Regions of interest (ROIs) are enlarged on the right. One tissue sample from each condition was utilized for Visium HD spatial transcriptomics based on similar morphological H&E staining with limited interindividual variability for n = 4 ( a ), n = 4 ( b ) and n = 5 ( c ) mice. d – h , Visium HD spatial transcriptomic of slides shown in a – c . Individual transcript localization is shown as log 2 -scaled heat maps of 8-μm bins for Ms4a1 ( d ), H2afx ( e ), Cd3g ( f ), Ccl21a ( g ) and Xbp1 ( h ). i , Graph-based subclustering of clusters of interest from sections in a – c were manually annotated and cross-validated with ACT and PanglaoDB cell annotation databases. IFZ, interfollicular zone; SCS, subcapsular sinus. Colours indicate cell type and anatomical zones.
    Figure Legend Snippet: a – c , H&E staining of formalin-fixed, paraffin-embedded (FFPE) spleen ( a ) and mesenteric lymph node ( b ) sections at 4 weeks post-LCMV infection and a liver section at 4 weeks post-RHV infection ( c ). Regions of interest (ROIs) are enlarged on the right. One tissue sample from each condition was utilized for Visium HD spatial transcriptomics based on similar morphological H&E staining with limited interindividual variability for n = 4 ( a ), n = 4 ( b ) and n = 5 ( c ) mice. d – h , Visium HD spatial transcriptomic of slides shown in a – c . Individual transcript localization is shown as log 2 -scaled heat maps of 8-μm bins for Ms4a1 ( d ), H2afx ( e ), Cd3g ( f ), Ccl21a ( g ) and Xbp1 ( h ). i , Graph-based subclustering of clusters of interest from sections in a – c were manually annotated and cross-validated with ACT and PanglaoDB cell annotation databases. IFZ, interfollicular zone; SCS, subcapsular sinus. Colours indicate cell type and anatomical zones.

    Techniques Used: Staining, Formalin-fixed Paraffin-Embedded, Infection

    (A-F) Visium HD spatial transcriptomic outputs at 4 weeks post-RHV infection in the liver displayed as log2-scaled heatmaps of 8 μm bins for single-parameter panels and feature sums for multiple-parameter lists. (A) Transcripts characteristic of central zone (zone 3) are shown in orange ( Glul, Cyp2e1 ) while those characteristic of portal zone (zone 1) are shown in green ( Hal, Arg1 ). (B) Co-expression of central (orange) and portal (green) zone-related transcripts shown in (A) as combined feature sums. (C) Merged expression of central (red, Glul and Cyp2e1 ) and portal (green, Hal and Arg1 ) combined transcripts. (D) Expression of various plasma cell-related transcripts as shown in blue ( Xbp1 , Derlr3 , Jchain , Irf4 ). (E) Merged expression of transcripts indicative of the central zone (red, Glul and Cyp2e1 ) and plasma cells ( Xbp1 , Derl3 , Jchain , Irf4 ). (F) Merged expression of transcripts indicative of the portal zone (green, Hal and Arg1 ) and plasma cells ( Xbp1 , Derl3 , Jchain , Irf4 ). (F) Co-expression of plasma cell-related transcripts ( Xbp1 , Derl3 , Jchain , Irf4 ) as feature sum list. (A, F) From morphologically similar H&E staining with limited interindividual variability conducted on n = 5 mice, data is shown from n = 1 mouse liver tissue with which Visium HD spatial transcriptomics was conducted.
    Figure Legend Snippet: (A-F) Visium HD spatial transcriptomic outputs at 4 weeks post-RHV infection in the liver displayed as log2-scaled heatmaps of 8 μm bins for single-parameter panels and feature sums for multiple-parameter lists. (A) Transcripts characteristic of central zone (zone 3) are shown in orange ( Glul, Cyp2e1 ) while those characteristic of portal zone (zone 1) are shown in green ( Hal, Arg1 ). (B) Co-expression of central (orange) and portal (green) zone-related transcripts shown in (A) as combined feature sums. (C) Merged expression of central (red, Glul and Cyp2e1 ) and portal (green, Hal and Arg1 ) combined transcripts. (D) Expression of various plasma cell-related transcripts as shown in blue ( Xbp1 , Derlr3 , Jchain , Irf4 ). (E) Merged expression of transcripts indicative of the central zone (red, Glul and Cyp2e1 ) and plasma cells ( Xbp1 , Derl3 , Jchain , Irf4 ). (F) Merged expression of transcripts indicative of the portal zone (green, Hal and Arg1 ) and plasma cells ( Xbp1 , Derl3 , Jchain , Irf4 ). (F) Co-expression of plasma cell-related transcripts ( Xbp1 , Derl3 , Jchain , Irf4 ) as feature sum list. (A, F) From morphologically similar H&E staining with limited interindividual variability conducted on n = 5 mice, data is shown from n = 1 mouse liver tissue with which Visium HD spatial transcriptomics was conducted.

    Techniques Used: Infection, Expressing, Clinical Proteomics, Staining

    a – c , Visium HD spatial transcriptomics from liver tissue at four weeks post-RHV infection. a , Transcript feature sums of log 2 -scaled heat maps of 8-μm bins for osteopontin ( Spp1 ), Cxcl12 , type I collagen ( Col1a1 and Col1a2 ( Col1a1/2 )), Icam2 , fibronectin ( Fn1 ), Cd44 , Cxcr4 , CD138 ( Sdc1 ), LFA-1 ( Itga4 / Itgb1 ) and VLA-4 ( Itgal/Itgb7 ). b , Merged transcript localization of feature sum lists from a . c , H&E image with portal vein (blue) and central vein (yellow) ROIs (left) with associated transcript localization (right). d , Cartoon diagram representing plausible molecular factors responsible for intrahepatic plasma cell retention. LSEC, liver sinusoidal endothelial cell. Created in BioRender. Grakoui, A. (2025) https://BioRender.com/ppmu1j5 . e , f , Intrahepatic total ( e ) and E2-specific ( f ) ASCs at 4 weeks post-infection with or without acute blockade of anchoring molecules at days 26 and 27 post-infection. AMD, AMD3100; anti-V/L, anti-VLA-4 plus anti-LFA-1; anti-V/L/S, anti-VLA-4, anti-LFA-1 plus anti-SPP1. n = 2 independent experiments. Control versus anti-V/L + AMD: P = 0.0003 ( e ), P = 0.0182 ( f ). g – i , Xenium Prime 5K spatial transcriptomics on liver tissue at three weeks post-infection with upstream morphological staining ( g ), virus, vasculature and plasma cell transcript localization ( h ), and virus, GC-associated and plasma cell transcript localization in periportal regions ( i ). j , RHV RNA in serum plotted against intrahepatic E2-specific ASC frequencies at four weeks post-infection. μMT, B6.129S2-Ighmtm1Cgn/J mice lacking mature B cells; dpi, days post infection. k , l , Bulk IgH BCR sequencing at 4 weeks post-infection from n = 3 RHV-infected mice, n = 3 LCMV-infected mice and n = 1 naive mouse. SHM accrual is plotted as nucleotide divergence from germline sequences among distinct clonotypes ( k ) and IgH V–J gene pairing chord diagrams ( l ). m – o , Intrahepatic common Igkc transcript localization alongside unique Igkv gene family transcripts with upstream morphological staining ( m ) and segmented cell borders showing transcript localization of Igkc with Igkv4-51 ( n ) and Igkc with Igkv15-103 ( o ). e , f , j , Data are representative or pooled values from at least two independent experiments of at least three mice per group. e , f , k , Data are mean + s.e.m. One-way ANOVA with Tukey’s multiple comparisons test ( e , f , k ); two-tailed nonparametric Spearman correlations with Pearson’s r ( j ).
    Figure Legend Snippet: a – c , Visium HD spatial transcriptomics from liver tissue at four weeks post-RHV infection. a , Transcript feature sums of log 2 -scaled heat maps of 8-μm bins for osteopontin ( Spp1 ), Cxcl12 , type I collagen ( Col1a1 and Col1a2 ( Col1a1/2 )), Icam2 , fibronectin ( Fn1 ), Cd44 , Cxcr4 , CD138 ( Sdc1 ), LFA-1 ( Itga4 / Itgb1 ) and VLA-4 ( Itgal/Itgb7 ). b , Merged transcript localization of feature sum lists from a . c , H&E image with portal vein (blue) and central vein (yellow) ROIs (left) with associated transcript localization (right). d , Cartoon diagram representing plausible molecular factors responsible for intrahepatic plasma cell retention. LSEC, liver sinusoidal endothelial cell. Created in BioRender. Grakoui, A. (2025) https://BioRender.com/ppmu1j5 . e , f , Intrahepatic total ( e ) and E2-specific ( f ) ASCs at 4 weeks post-infection with or without acute blockade of anchoring molecules at days 26 and 27 post-infection. AMD, AMD3100; anti-V/L, anti-VLA-4 plus anti-LFA-1; anti-V/L/S, anti-VLA-4, anti-LFA-1 plus anti-SPP1. n = 2 independent experiments. Control versus anti-V/L + AMD: P = 0.0003 ( e ), P = 0.0182 ( f ). g – i , Xenium Prime 5K spatial transcriptomics on liver tissue at three weeks post-infection with upstream morphological staining ( g ), virus, vasculature and plasma cell transcript localization ( h ), and virus, GC-associated and plasma cell transcript localization in periportal regions ( i ). j , RHV RNA in serum plotted against intrahepatic E2-specific ASC frequencies at four weeks post-infection. μMT, B6.129S2-Ighmtm1Cgn/J mice lacking mature B cells; dpi, days post infection. k , l , Bulk IgH BCR sequencing at 4 weeks post-infection from n = 3 RHV-infected mice, n = 3 LCMV-infected mice and n = 1 naive mouse. SHM accrual is plotted as nucleotide divergence from germline sequences among distinct clonotypes ( k ) and IgH V–J gene pairing chord diagrams ( l ). m – o , Intrahepatic common Igkc transcript localization alongside unique Igkv gene family transcripts with upstream morphological staining ( m ) and segmented cell borders showing transcript localization of Igkc with Igkv4-51 ( n ) and Igkc with Igkv15-103 ( o ). e , f , j , Data are representative or pooled values from at least two independent experiments of at least three mice per group. e , f , k , Data are mean + s.e.m. One-way ANOVA with Tukey’s multiple comparisons test ( e , f , k ); two-tailed nonparametric Spearman correlations with Pearson’s r ( j ).

    Techniques Used: Infection, Clinical Proteomics, Control, Staining, Virus, Sequencing, Two Tailed Test

    (A) Number of total IgG + ASCs in the liver at week 4 post-RHV infection following splenectomy one week prior to infection or FTY720 administration beginning at day 11 post-infection onward with representative ELISpot image. (B) Correlation between % plasma cells (CD38 low CD138 + of total B cells) and % GC B cells (CD38 low CD95 + of total B cells) in the liver at 4 weeks post-infection with RHV. (C) Representative H&E staining of FFPE sections from spleen at week 4 post-LCMV infection and liver at week 4 post-RHV infection. (D) Immunofluorescence staining of FFPE sections at 4 weeks post-RHV infection. Localization of representative Ig kappa gene families displayed as log2-scaled heatmaps of 8 μm bins at 4 weeks post-infection in (E) spleen (LCMV), (F) mesenteric lymph nodes (LCMV) and (G) liver (RHV). (H) From liver tissue at 4 weeks post-infection with RHV following FTY720 treatment, H&E (top) is shown for corresponding ROIs where Igkv19–93 localization is shown as log2-scaled heatmaps of 8 μm bins (bottom). (I) Correlation between intrahepatic CD38 low CD95 + GC B cells and RHV serum viremia at 4 weeks post-infection. (A-B) Data shown are representative or pooled values from 2-3 independent experiments of 3–9 mice per group. Visium HD spatial transcriptomics was conducted with liver tissue from n = 1 representative mouse following similar H&E morphological staining with limited interindividual variability from (C) n = 4 (spleen) and n = 4 (liver), (E) n = 4, (F) n = 4, (G) n = 5, and (H) n = 4 mice. (D) Representative image shown from immunofluorescent staining that was performed with liver tissue from n = 4 mice. (A) Mean + SEM. Statistical tests performed were (A) one-way ANOVA with Tukey’s multiple comparisons test and (B, I) two-tailed nonparametric Spearman correlation with Pearson’s r coefficient. (A) Uninfected vs. WT: p < 0.0001, WT vs. FTY720 D + 11: p = 0.9939, FTY720 D + 11 vs. Splenectomy: p = 0.9853. Statistical significance was denoted as ****=(p ≤ 0.0001).
    Figure Legend Snippet: (A) Number of total IgG + ASCs in the liver at week 4 post-RHV infection following splenectomy one week prior to infection or FTY720 administration beginning at day 11 post-infection onward with representative ELISpot image. (B) Correlation between % plasma cells (CD38 low CD138 + of total B cells) and % GC B cells (CD38 low CD95 + of total B cells) in the liver at 4 weeks post-infection with RHV. (C) Representative H&E staining of FFPE sections from spleen at week 4 post-LCMV infection and liver at week 4 post-RHV infection. (D) Immunofluorescence staining of FFPE sections at 4 weeks post-RHV infection. Localization of representative Ig kappa gene families displayed as log2-scaled heatmaps of 8 μm bins at 4 weeks post-infection in (E) spleen (LCMV), (F) mesenteric lymph nodes (LCMV) and (G) liver (RHV). (H) From liver tissue at 4 weeks post-infection with RHV following FTY720 treatment, H&E (top) is shown for corresponding ROIs where Igkv19–93 localization is shown as log2-scaled heatmaps of 8 μm bins (bottom). (I) Correlation between intrahepatic CD38 low CD95 + GC B cells and RHV serum viremia at 4 weeks post-infection. (A-B) Data shown are representative or pooled values from 2-3 independent experiments of 3–9 mice per group. Visium HD spatial transcriptomics was conducted with liver tissue from n = 1 representative mouse following similar H&E morphological staining with limited interindividual variability from (C) n = 4 (spleen) and n = 4 (liver), (E) n = 4, (F) n = 4, (G) n = 5, and (H) n = 4 mice. (D) Representative image shown from immunofluorescent staining that was performed with liver tissue from n = 4 mice. (A) Mean + SEM. Statistical tests performed were (A) one-way ANOVA with Tukey’s multiple comparisons test and (B, I) two-tailed nonparametric Spearman correlation with Pearson’s r coefficient. (A) Uninfected vs. WT: p < 0.0001, WT vs. FTY720 D + 11: p = 0.9939, FTY720 D + 11 vs. Splenectomy: p = 0.9853. Statistical significance was denoted as ****=(p ≤ 0.0001).

    Techniques Used: Infection, Enzyme-linked Immunospot, Clinical Proteomics, Staining, Immunofluorescence, Two Tailed Test

    a , b , Xenium Prime 5K spatial transcriptomics of liver tissue from healthy, AIH, HBV-infected and HCV-infected humans with upstream staining ( a ) and selected transcript localization ( b ). c – g , Quantitative analyses from spatial transcriptomics demonstrating number of leukocytic aggregates per mm 2 of tissue ( c ), aggregate area of leukocytic aggregates ( d ), and lymphocytic cell-type proportions of B cells ( e ), CD4 + T cells ( f ) and CD8 + T cells ( g ) observed in leukocytic aggregates from individuals with AIH ( n = 1), chronic HBV ( n = 2) and chronic HCV ( n = 2) infection. Data are mean + s.e.m. d – g , One-way ANOVA with Tukey’s multiple comparisons test. AIH versus HBV: P = 0.0101 ( g ). h , Quantification of cell types and their direct contact partners within leukocytic aggregates from annotated spatial transcriptomics with subcellular resolution and cell segmentation during mouse RHV (orange) and human HCV (blue) infection. HSC, hepatic stellate cell. i – n , RHV-infected mouse liver ( i , k , m ) and HCV-infected human liver ( j , l , n ) tissue. Generative GC-like structures were characterized upstream staining ( i , j ) and GC-associated transcript localization ( k , l ) and colour-coded cell-type annotation with selected overlaid transcripts ( m , n ). o – t , RHV-infected mouse liver ( o , q , s ) and HCV-infected human liver ( p , r , t ) tissue. Areas of intrahepatic plasma cell residency were characterized by upstream staining ( o , p ) and plasma cell and hepatic stellate cell and fibroblast-associated transcripts ( q , r ) with colour-coded cell-type annotation ( s , t ). Based on similar morphological H&E staining with limited interindividual variability of n = 2 HCV-infected humans and n = 4 RHV-infected mice, Xenium 5K was performed on tissue from n = 2 human and n = 1 mouse livers, from which n = 1 representative tissue of each are shown in i – t .
    Figure Legend Snippet: a , b , Xenium Prime 5K spatial transcriptomics of liver tissue from healthy, AIH, HBV-infected and HCV-infected humans with upstream staining ( a ) and selected transcript localization ( b ). c – g , Quantitative analyses from spatial transcriptomics demonstrating number of leukocytic aggregates per mm 2 of tissue ( c ), aggregate area of leukocytic aggregates ( d ), and lymphocytic cell-type proportions of B cells ( e ), CD4 + T cells ( f ) and CD8 + T cells ( g ) observed in leukocytic aggregates from individuals with AIH ( n = 1), chronic HBV ( n = 2) and chronic HCV ( n = 2) infection. Data are mean + s.e.m. d – g , One-way ANOVA with Tukey’s multiple comparisons test. AIH versus HBV: P = 0.0101 ( g ). h , Quantification of cell types and their direct contact partners within leukocytic aggregates from annotated spatial transcriptomics with subcellular resolution and cell segmentation during mouse RHV (orange) and human HCV (blue) infection. HSC, hepatic stellate cell. i – n , RHV-infected mouse liver ( i , k , m ) and HCV-infected human liver ( j , l , n ) tissue. Generative GC-like structures were characterized upstream staining ( i , j ) and GC-associated transcript localization ( k , l ) and colour-coded cell-type annotation with selected overlaid transcripts ( m , n ). o – t , RHV-infected mouse liver ( o , q , s ) and HCV-infected human liver ( p , r , t ) tissue. Areas of intrahepatic plasma cell residency were characterized by upstream staining ( o , p ) and plasma cell and hepatic stellate cell and fibroblast-associated transcripts ( q , r ) with colour-coded cell-type annotation ( s , t ). Based on similar morphological H&E staining with limited interindividual variability of n = 2 HCV-infected humans and n = 4 RHV-infected mice, Xenium 5K was performed on tissue from n = 2 human and n = 1 mouse livers, from which n = 1 representative tissue of each are shown in i – t .

    Techniques Used: Infection, Staining, Clinical Proteomics

    Xenium Prime 5 K spatial transcriptomics was performed with liver tissue obtained during human (A, B) AIH and (C, D) HBV infection. Depicted are regions of interest showing (A, C) upstream morphological staining and (B, D) expression of various color-coded transcripts and annotated cell types. Data shown from (A, B) n = 1 individual with AIH and (C, D) n = 1 individual chronically infected with HBV from which liver tissue was selected for spatial transcriptomics conducted on (A, B) n = 1 individual and (C, D) n = 2 individuals with limited interindividual variability.
    Figure Legend Snippet: Xenium Prime 5 K spatial transcriptomics was performed with liver tissue obtained during human (A, B) AIH and (C, D) HBV infection. Depicted are regions of interest showing (A, C) upstream morphological staining and (B, D) expression of various color-coded transcripts and annotated cell types. Data shown from (A, B) n = 1 individual with AIH and (C, D) n = 1 individual chronically infected with HBV from which liver tissue was selected for spatial transcriptomics conducted on (A, B) n = 1 individual and (C, D) n = 2 individuals with limited interindividual variability.

    Techniques Used: Infection, Staining, Expressing

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    Article Snippet: .. Doxycycline-treated retinas were analyzed using Xenium 5K spatial transcriptomics , and cellular age was determined using our Xenium-based aging clock. ..

    Article Title: Spatial Transcriptomics Identify T Cell-Driven Mechanisms of Kidney Damage in Immune Checkpoint Inhibitor-Associated Acute Interstitial Nephritis
    Article Snippet: .. Here, we utilized Xenium Prime 5K, a novel spatial transcriptomics technology, to compare and contrast the cellular composition of kidney biopsy specimens from patients with ICI-AIN versus ICI-ATN and identify new mechanisms of kidney damage. ..

    Article Title: iHALT unlocks liver functionality as a surrogate secondary lymphoid organ
    Article Snippet: .. Fig. 5 Hepaciviral infection in mouse and human induce intrahepatic lymphoid structures with highly similar cellular composition, organizational microarchitecture and cell–cell contacts. a , b , Xenium Prime 5K spatial transcriptomics of liver tissue from healthy, AIH, HBV-infected and HCV-infected humans with upstream staining ( a ) and selected transcript localization ( b ). c – g , Quantitative analyses from spatial transcriptomics demonstrating number of leukocytic aggregates per mm of tissue ( c ), aggregate area of leukocytic aggregates ( d ), and lymphocytic cell-type proportions of B cells ( e ), CD4 + T cells ( f ) and CD8 + T cells ( g ) observed in leukocytic aggregates from individuals with AIH ( n = 1), chronic HBV ( n = 2) and chronic HCV ( n = 2) infection. ..

    Imaging:

    Article Title: Spatial transcriptomic profiling of decalcified murine musculoskeletal samples via Xenium Prime 5K
    Article Snippet: .. Imaging-based spatial transcriptomics technologies, including Xenium Prime 5K, generally yield fewer detected transcripts per cell compared to sequencing-based approaches, such as Visium . ..

    Sequencing:

    Article Title: Spatial transcriptomic profiling of decalcified murine musculoskeletal samples via Xenium Prime 5K
    Article Snippet: .. Imaging-based spatial transcriptomics technologies, including Xenium Prime 5K, generally yield fewer detected transcripts per cell compared to sequencing-based approaches, such as Visium . ..

    Infection:

    Article Title: iHALT unlocks liver functionality as a surrogate secondary lymphoid organ
    Article Snippet: .. Fig. 5 Hepaciviral infection in mouse and human induce intrahepatic lymphoid structures with highly similar cellular composition, organizational microarchitecture and cell–cell contacts. a , b , Xenium Prime 5K spatial transcriptomics of liver tissue from healthy, AIH, HBV-infected and HCV-infected humans with upstream staining ( a ) and selected transcript localization ( b ). c – g , Quantitative analyses from spatial transcriptomics demonstrating number of leukocytic aggregates per mm of tissue ( c ), aggregate area of leukocytic aggregates ( d ), and lymphocytic cell-type proportions of B cells ( e ), CD4 + T cells ( f ) and CD8 + T cells ( g ) observed in leukocytic aggregates from individuals with AIH ( n = 1), chronic HBV ( n = 2) and chronic HCV ( n = 2) infection. ..

    Staining:

    Article Title: iHALT unlocks liver functionality as a surrogate secondary lymphoid organ
    Article Snippet: .. Fig. 5 Hepaciviral infection in mouse and human induce intrahepatic lymphoid structures with highly similar cellular composition, organizational microarchitecture and cell–cell contacts. a , b , Xenium Prime 5K spatial transcriptomics of liver tissue from healthy, AIH, HBV-infected and HCV-infected humans with upstream staining ( a ) and selected transcript localization ( b ). c – g , Quantitative analyses from spatial transcriptomics demonstrating number of leukocytic aggregates per mm of tissue ( c ), aggregate area of leukocytic aggregates ( d ), and lymphocytic cell-type proportions of B cells ( e ), CD4 + T cells ( f ) and CD8 + T cells ( g ) observed in leukocytic aggregates from individuals with AIH ( n = 1), chronic HBV ( n = 2) and chronic HCV ( n = 2) infection. ..



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    a Schematic diagram of the spatial <t>transcriptome</t> analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.
    Xenium Spatial Transcriptome Analysis, supplied by 10X Genomics, 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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    xenium spatial transcriptome analysis - by Bioz Stars, 2026-10
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    xenium in situ spatial transcriptomic analysis  (10X Genomics)
    86
    10X Genomics xenium in situ spatial transcriptomic analysis
    a Schematic diagram of the spatial <t>transcriptome</t> analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.
    Xenium In Situ Spatial Transcriptomic Analysis, supplied by 10X Genomics, 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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    Average 86 stars, based on 1 article reviews
    xenium in situ spatial transcriptomic analysis - by Bioz Stars, 2026-10
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    10x xenium spatial transcriptomics analysis  (Spatial Transcriptomics Inc)
    90
    Spatial Transcriptomics Inc 10x xenium spatial transcriptomics analysis
    a Schematic diagram of the spatial <t>transcriptome</t> analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.
    10x Xenium Spatial Transcriptomics Analysis, supplied by Spatial Transcriptomics Inc, 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/xenium+spatial+transcriptome+analysis/10x+spatial+transcriptomics/pm40593805-158-11-0
    Average 90 stars, based on 1 article reviews
    10x xenium spatial transcriptomics analysis - by Bioz Stars, 2026-10
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    xenium-based spatial transcriptomics analysis  (Spatial Transcriptomics Inc)
    90
    Spatial Transcriptomics Inc xenium-based spatial transcriptomics analysis
    Xenium-Based Spatial <t>Transcriptomics</t> Analysis of TLE and Control Mouse Brain Sections. A Whole-brain transcriptomic information obtained through Xenium-based spatial transcriptomics analysis, with reconstructed cell bodies displayed in different colours. The white box highlights the TLE and control hippocampal regions. B Enlarged view of the hippocampal region highlighted in A. C UMAP plot showing the 27 identified cell types. D - I High-resolution expression patterns of marker genes for astrocytes, microglia, oligodendrocytes, CA1 pyramidal neurons, dentate gyrus granule cells, and CA3 pyramidal neurons in Control and TLE sections. The left side represents the brain of a control mouse, while the right side represents the brain of a TLE mouse. Each red dot represents a positive expression point for a gene, with a diameter of 5 μm
    Xenium Based Spatial Transcriptomics Analysis, supplied by Spatial Transcriptomics Inc, 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/xenium+spatial+transcriptome+analysis/spatial+transcriptomics++st+/pmc11396644-186-3-3
    Average 90 stars, based on 1 article reviews
    xenium-based spatial transcriptomics analysis - by Bioz Stars, 2026-10
    90/100 stars
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    a Schematic diagram of the spatial transcriptome analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.

    Journal: bioRxiv

    Article Title: CXCL10 drives female-specific tau pathology progression and defines sex-dependent vulnerability in tauopathy model mice

    doi: 10.64898/2026.04.19.719088

    Figure Lengend Snippet: a Schematic diagram of the spatial transcriptome analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.

    Article Snippet: FFPE brain sections were analyzed using Xenium spatial transcriptome analysis (10x Genomics).

    Techniques: Formalin-fixed Paraffin-Embedded, Olfactory, Gene Expression

    Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections. A Whole-brain transcriptomic information obtained through Xenium-based spatial transcriptomics analysis, with reconstructed cell bodies displayed in different colours. The white box highlights the TLE and control hippocampal regions. B Enlarged view of the hippocampal region highlighted in A. C UMAP plot showing the 27 identified cell types. D - I High-resolution expression patterns of marker genes for astrocytes, microglia, oligodendrocytes, CA1 pyramidal neurons, dentate gyrus granule cells, and CA3 pyramidal neurons in Control and TLE sections. The left side represents the brain of a control mouse, while the right side represents the brain of a TLE mouse. Each red dot represents a positive expression point for a gene, with a diameter of 5 μm

    Journal: Biomarker Research

    Article Title: Single-cell, single-nucleus and xenium-based spatial transcriptomics analyses reveal inflammatory activation and altered cell interactions in the hippocampus in mice with temporal lobe epilepsy

    doi: 10.1186/s40364-024-00636-3

    Figure Lengend Snippet: Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections. A Whole-brain transcriptomic information obtained through Xenium-based spatial transcriptomics analysis, with reconstructed cell bodies displayed in different colours. The white box highlights the TLE and control hippocampal regions. B Enlarged view of the hippocampal region highlighted in A. C UMAP plot showing the 27 identified cell types. D - I High-resolution expression patterns of marker genes for astrocytes, microglia, oligodendrocytes, CA1 pyramidal neurons, dentate gyrus granule cells, and CA3 pyramidal neurons in Control and TLE sections. The left side represents the brain of a control mouse, while the right side represents the brain of a TLE mouse. Each red dot represents a positive expression point for a gene, with a diameter of 5 μm

    Article Snippet: Fig. 6 Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections.

    Techniques: Control, Expressing, Marker