Spatial Transcriptomics:Article Title: 4R-tau seeding activity reveals molecular subtypes in progressive supranuclear palsy
Article Snippet: .. Fig. 7 Spatial transcriptomics reveals immune and neuronal dysregulation in high-seeder PSP cases. a H&E sections of the four slices of primary motor cortex assayed with Visium spatial transcriptomic. b Marker genes confirm manually annotated cortical layers. c Annotated cortical layers in each slide, white white matter, other colors are the same as in panel d. “Edge” indicates a region of stressed tissue found on the edge of the tissue sample. d Uniform Manifold Approximation and Projection (UMAP) shows annotated layers are transcriptionally distinct. e UMAP confirms successful integration of spatial transcriptomic profiles across slices. f Differentially expressed genes were identified using a negative binomial mixed-effect model, significant genes were identified (<5% FDR) and used for pathway analysis with GSEA. ..
Article Title: Serotonergic neuron-glioma interactions drive high-grade glioma pathophysiology
Article Snippet: .. Briefly, Spatial transcriptomics experiments were conducted on adult IDH wild-type glioblastoma and pediatric H3K27M diffuse midline glioma tumors using the 10X Visium Spatial Gene Expression kit, following the manufacturer’s protocol for tissue optimization and library preparation. ..
Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Article Title: Multiplex gene-editing strategy to engineer allogeneic EGFR-targeting CAR T-cells with improved efficacy against solid tumors
Article Snippet: Representative images from four individual tumors from 10 to 20 different cutting surfaces. c Quantification of hypoxia in various tumor regions within resected H226 tumors from NCG mice determined by mean fluorescence intensity (MFI) of Hypoxyprobe. .. Representative image of a resected tumor section; quantification was performed across 6 independent slides (3 tumors per slide from individual mice) with an average of 13.5 regions of interest (ROI) analyzed per slide. d Spatial transcriptomics gene expression analysis from hypoxic regions in ( c ) (white = low hypoxia, light green = medium hypoxia, dark green = high hypoxia). ..
Article Title: 4R-tau seeding activity reveals molecular subtypes in progressive supranuclear palsy.
Article Snippet: .. Spatial transcriptomics reveals immune and neuronal dysregulation in high-seeder PSP cases. (a) H & E sections of the four slices of primary motor cortex assayed with Visium spatial transcriptomic. (b) Marker genes confirm manually annotated cortical layers. (c) Annotated cortical layers in each slide, white = white matter, other colours are the same as in panel d. “Edge” indicates a region of stressed tissue found on the edge of the tissue sample. (d) Uniform Manifold Approximation and Projection (UMAP) show annotated layers are transcriptionally distinct. (e) UMAP confirms successful integration of spatial transcriptomic profiles across slices. (f) Differentially expressed genes were identified using a negative binomial mixed-effect model, significant genes were identified (<5% FDR) and used for pathway analysis with GSEA. ..
Marker:Article Title: 4R-tau seeding activity reveals molecular subtypes in progressive supranuclear palsy
Article Snippet: .. Fig. 7 Spatial transcriptomics reveals immune and neuronal dysregulation in high-seeder PSP cases. a H&E sections of the four slices of primary motor cortex assayed with Visium spatial transcriptomic. b Marker genes confirm manually annotated cortical layers. c Annotated cortical layers in each slide, white white matter, other colors are the same as in panel d. “Edge” indicates a region of stressed tissue found on the edge of the tissue sample. d Uniform Manifold Approximation and Projection (UMAP) shows annotated layers are transcriptionally distinct. e UMAP confirms successful integration of spatial transcriptomic profiles across slices. f Differentially expressed genes were identified using a negative binomial mixed-effect model, significant genes were identified (<5% FDR) and used for pathway analysis with GSEA. ..
Article Title: 4R-tau seeding activity reveals molecular subtypes in progressive supranuclear palsy.
Article Snippet: .. Spatial transcriptomics reveals immune and neuronal dysregulation in high-seeder PSP cases. (a) H & E sections of the four slices of primary motor cortex assayed with Visium spatial transcriptomic. (b) Marker genes confirm manually annotated cortical layers. (c) Annotated cortical layers in each slide, white = white matter, other colours are the same as in panel d. “Edge” indicates a region of stressed tissue found on the edge of the tissue sample. (d) Uniform Manifold Approximation and Projection (UMAP) show annotated layers are transcriptionally distinct. (e) UMAP confirms successful integration of spatial transcriptomic profiles across slices. (f) Differentially expressed genes were identified using a negative binomial mixed-effect model, significant genes were identified (<5% FDR) and used for pathway analysis with GSEA. ..
Gene Expression:
Article Title: Serotonergic neuron-glioma interactions drive high-grade glioma pathophysiology
Article Snippet: .. Briefly, Spatial transcriptomics experiments were conducted on adult IDH wild-type glioblastoma and pediatric H3K27M diffuse midline glioma tumors using the 10X Visium Spatial Gene Expression kit, following the manufacturer’s protocol for tissue optimization and library preparation. ..
Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Article Title: Multiplex gene-editing strategy to engineer allogeneic EGFR-targeting CAR T-cells with improved efficacy against solid tumors
Article Snippet: Representative images from four individual tumors from 10 to 20 different cutting surfaces. c Quantification of hypoxia in various tumor regions within resected H226 tumors from NCG mice determined by mean fluorescence intensity (MFI) of Hypoxyprobe. .. Representative image of a resected tumor section; quantification was performed across 6 independent slides (3 tumors per slide from individual mice) with an average of 13.5 regions of interest (ROI) analyzed per slide. d Spatial transcriptomics gene expression analysis from hypoxic regions in ( c ) (white = low hypoxia, light green = medium hypoxia, dark green = high hypoxia). ..
Expressing:Article Title: CHCHD2 mutant mice link mitochondrial deficits to PD pathophysiology
Article Snippet: .. Snap-frozen brain sections of CHCHD2 T61I and KO mice were analyzed by the Visium spatial transcriptomics kit. (A, B) Expression of DA neuron markers are confined to expected spatial regions. ..
RNA Sequencing:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Biomarker Discovery:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Immunohistochemistry:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Staining:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Imaging:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Cell Differentiation:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Cell Isolation:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Cell Culture:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Reverse Transcription:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Polymerase Chain Reaction:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Western Blot:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Isolation:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
Recombinant:Article Title: Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS • METHOD DETAILS ○ Spatial transcriptomics using Visium spatial gene expression ○ Preprocessing of spatial transcriptomic data ○ Spatial data integration and cell type identification ○ Generation of single-nucleus RNA sequencing data ○ Preprocessing of snRNA-seq data ○ snRNA-seq data integration and cell type identification ○ Data generation and processing of the validation cohort ○ Spatial deconvolution ○ Quantifying spatial neighborhood enrichment with SENSE ○ Pseudo-time analysis ○ Cell-cell communication analysis ○ Bulk deconvolution ○ IHC staining and imaging ○ Quantification of CES1 signal ○ Human adipose tissue-derived stromal cell differentiation and stim- ulation 12 Cell Metabolism 38, 1–15, February 3, 2026 ○ Adipose tissue-derived endothelial cell isolation and culture ○ THP1 cell culture ○ Magnetic bead separation and LPS stimulation of CD45 + cells ○ Gene expression analysis by quantitative reverse transcription PCR ○ Western blot ○ SAA quantification in conditioned media ○ Stromal-vascular fraction isolation for LPS and recombinant SAA treatment ○ Bulk RNA-seq data analysis of LPS and recombinant SAA treated samples ○ Gene set enrichment analysis • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. cmet.2025.12.008. ..
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