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Alcohol cessation promotes transcriptomic changes in hepatocytes and non-parenchymal cell clusters. Mice were fed ad libitum WD with 20% alcohol in the drinking water for 20 weeks (WDA). For disease resolution mice were placed then on chow diet with plain water for 4 weeks (Res). Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay <t>from</t> <t>Nanostrings</t> using <t>CosMx</t> platform. Cell boundary was assigned based on nuclear and membrane staining. Cells were analyzed using Seurat v5 package. ( A ) Top . Sirius red staining of the section adjacent to section used for transcriptional profiling. Bottom. UMAP plot of cell clusters. ( B and C ) Gene expression of genes enriched in individual clusters. ( D ) Cell abundance for each cluster across 45 FOVs. Average proportion for each cluster in WDA and Res FOVs (n = 22–23 per condition). ∗ Padj < .01; ∗∗∗ Padj < .0001. ( E ) Fold change for indicated gene transcripts between Res and WDA samples in males (M) and females (F).
Cosmx Platform, 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/result/cosmx platform/product/Spatial Transcriptomics Inc
Average 86 stars, based on 1 article reviews
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cosmx spatial molecular imaging (smi) platform  (Bruker Corporation)
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Alcohol cessation promotes transcriptomic changes in hepatocytes and non-parenchymal cell clusters. Mice were fed ad libitum WD with 20% alcohol in the drinking water for 20 weeks (WDA). For disease resolution mice were placed then on chow diet with plain water for 4 weeks (Res). Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay <t>from</t> <t>Nanostrings</t> using <t>CosMx</t> platform. Cell boundary was assigned based on nuclear and membrane staining. Cells were analyzed using Seurat v5 package. ( A ) Top . Sirius red staining of the section adjacent to section used for transcriptional profiling. Bottom. UMAP plot of cell clusters. ( B and C ) Gene expression of genes enriched in individual clusters. ( D ) Cell abundance for each cluster across 45 FOVs. Average proportion for each cluster in WDA and Res FOVs (n = 22–23 per condition). ∗ Padj < .01; ∗∗∗ Padj < .0001. ( E ) Fold change for indicated gene transcripts between Res and WDA samples in males (M) and females (F).
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https://www.bioz.com/result/cosmx spatial molecular imaging (smi) platform/product/Bruker Corporation
Average 90 stars, based on 1 article reviews
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cosmx spatial transcriptomics platform  (Spatial Transcriptomics Inc)
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Alcohol cessation promotes transcriptomic changes in hepatocytes and non-parenchymal cell clusters. Mice were fed ad libitum WD with 20% alcohol in the drinking water for 20 weeks (WDA). For disease resolution mice were placed then on chow diet with plain water for 4 weeks (Res). Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay <t>from</t> <t>Nanostrings</t> using <t>CosMx</t> platform. Cell boundary was assigned based on nuclear and membrane staining. Cells were analyzed using Seurat v5 package. ( A ) Top . Sirius red staining of the section adjacent to section used for transcriptional profiling. Bottom. UMAP plot of cell clusters. ( B and C ) Gene expression of genes enriched in individual clusters. ( D ) Cell abundance for each cluster across 45 FOVs. Average proportion for each cluster in WDA and Res FOVs (n = 22–23 per condition). ∗ Padj < .01; ∗∗∗ Padj < .0001. ( E ) Fold change for indicated gene transcripts between Res and WDA samples in males (M) and females (F).
Cosmx Spatial Transcriptomics Platform, 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/result/cosmx spatial transcriptomics platform/product/Spatial Transcriptomics Inc
Average 90 stars, based on 1 article reviews
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6,000-gene panels cosmx platform  (Bruker Corporation)
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Bruker Corporation 6,000-gene panels cosmx platform
Alcohol cessation promotes transcriptomic changes in hepatocytes and non-parenchymal cell clusters. Mice were fed ad libitum WD with 20% alcohol in the drinking water for 20 weeks (WDA). For disease resolution mice were placed then on chow diet with plain water for 4 weeks (Res). Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay <t>from</t> <t>Nanostrings</t> using <t>CosMx</t> platform. Cell boundary was assigned based on nuclear and membrane staining. Cells were analyzed using Seurat v5 package. ( A ) Top . Sirius red staining of the section adjacent to section used for transcriptional profiling. Bottom. UMAP plot of cell clusters. ( B and C ) Gene expression of genes enriched in individual clusters. ( D ) Cell abundance for each cluster across 45 FOVs. Average proportion for each cluster in WDA and Res FOVs (n = 22–23 per condition). ∗ Padj < .01; ∗∗∗ Padj < .0001. ( E ) Fold change for indicated gene transcripts between Res and WDA samples in males (M) and females (F).
6,000 Gene Panels Cosmx Platform, supplied by Bruker Corporation, 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/result/6,000-gene panels cosmx platform/product/Bruker Corporation
Average 90 stars, based on 1 article reviews
6,000-gene panels cosmx platform - by Bioz Stars, 2026-06
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cosmx platform  (Bruker Corporation)
90
Bruker Corporation cosmx platform
Alcohol cessation promotes transcriptomic changes in hepatocytes and non-parenchymal cell clusters. Mice were fed ad libitum WD with 20% alcohol in the drinking water for 20 weeks (WDA). For disease resolution mice were placed then on chow diet with plain water for 4 weeks (Res). Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay <t>from</t> <t>Nanostrings</t> using <t>CosMx</t> platform. Cell boundary was assigned based on nuclear and membrane staining. Cells were analyzed using Seurat v5 package. ( A ) Top . Sirius red staining of the section adjacent to section used for transcriptional profiling. Bottom. UMAP plot of cell clusters. ( B and C ) Gene expression of genes enriched in individual clusters. ( D ) Cell abundance for each cluster across 45 FOVs. Average proportion for each cluster in WDA and Res FOVs (n = 22–23 per condition). ∗ Padj < .01; ∗∗∗ Padj < .0001. ( E ) Fold change for indicated gene transcripts between Res and WDA samples in males (M) and females (F).
Cosmx Platform, supplied by Bruker Corporation, 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/result/cosmx platform/product/Bruker Corporation
Average 90 stars, based on 1 article reviews
cosmx platform - by Bioz Stars, 2026-06
90/100 stars
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cosmx smi platform  (Bruker Corporation)
90
Bruker Corporation cosmx smi platform
Alcohol cessation promotes transcriptomic changes in hepatocytes and non-parenchymal cell clusters. Mice were fed ad libitum WD with 20% alcohol in the drinking water for 20 weeks (WDA). For disease resolution mice were placed then on chow diet with plain water for 4 weeks (Res). Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay <t>from</t> <t>Nanostrings</t> using <t>CosMx</t> platform. Cell boundary was assigned based on nuclear and membrane staining. Cells were analyzed using Seurat v5 package. ( A ) Top . Sirius red staining of the section adjacent to section used for transcriptional profiling. Bottom. UMAP plot of cell clusters. ( B and C ) Gene expression of genes enriched in individual clusters. ( D ) Cell abundance for each cluster across 45 FOVs. Average proportion for each cluster in WDA and Res FOVs (n = 22–23 per condition). ∗ Padj < .01; ∗∗∗ Padj < .0001. ( E ) Fold change for indicated gene transcripts between Res and WDA samples in males (M) and females (F).
Cosmx Smi Platform, supplied by Bruker Corporation, 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/result/cosmx smi platform/product/Bruker Corporation
Average 90 stars, based on 1 article reviews
cosmx smi platform - by Bioz Stars, 2026-06
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Alcohol cessation promotes transcriptomic changes in hepatocytes and non-parenchymal cell clusters. Mice were fed ad libitum WD with 20% alcohol in the drinking water for 20 weeks (WDA). For disease resolution mice were placed then on chow diet with plain water for 4 weeks (Res). Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay from Nanostrings using CosMx platform. Cell boundary was assigned based on nuclear and membrane staining. Cells were analyzed using Seurat v5 package. ( A ) Top . Sirius red staining of the section adjacent to section used for transcriptional profiling. Bottom. UMAP plot of cell clusters. ( B and C ) Gene expression of genes enriched in individual clusters. ( D ) Cell abundance for each cluster across 45 FOVs. Average proportion for each cluster in WDA and Res FOVs (n = 22–23 per condition). ∗ Padj < .01; ∗∗∗ Padj < .0001. ( E ) Fold change for indicated gene transcripts between Res and WDA samples in males (M) and females (F).

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: Acute Phase Response-driven Hepatic Niche Remodeling Promotes Fibrosis Resolution After Alcohol Cessation

doi: 10.1016/j.jcmgh.2025.101689

Figure Lengend Snippet: Alcohol cessation promotes transcriptomic changes in hepatocytes and non-parenchymal cell clusters. Mice were fed ad libitum WD with 20% alcohol in the drinking water for 20 weeks (WDA). For disease resolution mice were placed then on chow diet with plain water for 4 weeks (Res). Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay from Nanostrings using CosMx platform. Cell boundary was assigned based on nuclear and membrane staining. Cells were analyzed using Seurat v5 package. ( A ) Top . Sirius red staining of the section adjacent to section used for transcriptional profiling. Bottom. UMAP plot of cell clusters. ( B and C ) Gene expression of genes enriched in individual clusters. ( D ) Cell abundance for each cluster across 45 FOVs. Average proportion for each cluster in WDA and Res FOVs (n = 22–23 per condition). ∗ Padj < .01; ∗∗∗ Padj < .0001. ( E ) Fold change for indicated gene transcripts between Res and WDA samples in males (M) and females (F).

Article Snippet: Spatial transcriptomics analysis of livers from these mice (n = 2 per group, males) using 1000-plex assay from Nanostrings using CosMx platform.

Techniques: Plex Assay, Membrane, Staining, Gene Expression