image image | caption string | subfigures list |
|---|---|---|
The relationship between prognosis and clinicopathological parameters in four independent cohorts (*p < 0.05; **p < 0.01; ***p < 0.001). (A-D) The distribution of AMI, biochemical recurrence status along with bRFS times of PCa patients and heatmaps of 8 key prognostic AME regulators. (E-H) Kaplan-Meier survival curves ... | [
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"caption": "The relationship between prognosis and clinicopathological parameters in four independent cohorts (*p < 0.05; **p < 0.01; ***p < 0.001). The distribution of AMI, biochemical recurrence status along... | |
SR-DGN identifies complex tissue structures in the Slide-seqV2 mouse hippocampus dataset. (A) Annotation of the Slide-seqV2 mouse hippocampus structure from the Allen Reference Atlas. (B) Spatial clustering results of SR-DGN, SCANPY, STAGATE, GraphST, SpaceFlow, and SEDR in the Slide-seqV2 mouse hippocampus dataset. (C... | [
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"caption": "SR-DGN identifies complex tissue structures in the Slide-seqV2 mouse hippocampus dataset. Violin plots of the two genes."
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Cell-type deconvolution results for 10X Visium human breast cancer (block A section 1) data. a Scatter pie plots displaying the cell-type proportion estimates of SpaDecon, RCTD, SPOTlight, Stereoscope, and cell2location at each spot, along with heatmaps showing the estimated distributions of cancer epithelial, B, and T... | [
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"caption": "Cell-type deconvolution results for 10X Visium human breast cancer (block A section 1) data. Low-resolution histology image of breast cancer tissue section from which Visium data were ... | |
Mapping of gene signatures ER stress and immune cells on CRC ST data. (A) The enrichment score of GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS gene set on ST data; the dotted line represents the tumor region. (B) Enrichment score of DEGs between ERcluster A and B on ST data. (C–F) Enrichment score of FOXP3+ Treg, CAFs... | [
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"caption": "Mapping of gene signatures ER stress and immune cells on CRC ST data. Enrichment score of MDSC signature on ST data."
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Deconvolution methods performance on different reference and bulk datasets. Bar plots comparing the features of the three snRNA-seq datasets used as references in deconvolution, noting: A. number of donors and diagnosis, B. total number of nuclei, and C. overall cell type composition. D. Scatter plot of cell type propo... | [
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"caption": "Deconvolution methods performance on different reference and bulk datasets. Scatter plot of cell type proportions estimated by RNAScope/IF (x-axis) vs. the predicted cell type p... | |
Dimensionality Reduction and Clustering. A) UMAP of integrated samples displaying 7 clusters identified in the merged and integrated PT #1 & PT #2 samples. B) Visualization of integrated clusters projected onto each sample identity. PT#1 is on the left and PT#2 is on the right. C) Heatmap of the top three upregulated (... | [
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"caption": "Dimensionality Reduction and Clustering. UMAP of integrated samples displaying 7 clusters identified in the merged and integrated PT #1 & PT #2 samples."
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GeneSurfer is an interactive interface for exploring local gene expression patterns in the spatial domain. A. Overview of the proposed workflow. Users select transcriptomically similar cells and visualize them in 3D. Genes are filtered and then clustered based on their expression within the selected cells. GO terms are... | [
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"caption": "GeneSurfer is an interactive interface for exploring local gene expression patterns in the spatial domain. Overview of the proposed workflow. Users select transcriptomically similar cells and visualize them i... | |
STRING as well as upstream regulator analyses cluster around inflammatory processes during the priming phase of human LR. (A) STRING analyses (including only significantly regulated genes with a fold change of >1.5) are illustrated for individuals with and without postoperative DLR and colour coded according to the deg... | [
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"caption": "STRING as well as upstream regulator analyses cluster around inflammatory processes during the priming phase of human LR. IPA upstream regulator assessment is illustrated for individuals ... | |
Single-cell sequencing analysis of SPP1 expression in relation to CAF infiltration. (A): Annotated UMAP clustering map for single-cell objects. (B): Identification of classical marker gene expression levels across various cell types. (C): Bar chart showing the percentage of cell types within the 12 samples in a single-... | [
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"caption": "Single-cell sequencing analysis of SPP1 expression in relation to CAF infiltration. Violin plots displaying SPP1 expression in different cell types."
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0... | |
Spatial transcriptomic analysis of estrogen-receptor-positive and triple-negative breast cancer patients (A) Scatterplot showing the position of the estrogen-receptor-positive (ER+) and triple-negative breast cancer (TNBC) patients on a two-dimensional luminal-basal plane. Each point in the plane is based on the gene e... | [
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"caption": "Spatial transcriptomic analysis of estrogen-receptor-positive and triple-negative breast cancer patients. Scatterplot showing the position of the estrogen-receptor-positive (ER+) and tripl... | |
Cell-cell interaction analysis in HCC and T cells. (A) The number and strength of interaction pathways among eight cell types. (B) Bubble plot showing specific pathways of the eight cell-cell interactions. (C) Hierarchical plot showing the inferred intercellular communication network for SPP1 signaling, indicating the ... | [
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"caption": "Cell-cell interaction analysis in HCC and T cells. Heatmap depicting the SPP1 signaling pathways to evaluate each cell type’s involvement in cell interaction, showing the relative import... | |
Enrichment for tissue state B is independently associated with worse survival. a Pre-ranked Gene Set Enrichment Analysis (GSEA) comparing tissue state B bulk RNAseq samples with tissue states A & C samples for 3 sub-lineages: Ast3, moTAM, and T-cells. Marker genes for each cell type were used as the gene set for each a... | [
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"caption": "Enrichment for tissue state B is independently associated with worse survival. Cox proportional hazard ratio of survival in the combined TCGA and CGGA IDH-WT GBM dataset given enrich... | |
Visualization results of datasets at spot resolution. (a) Visualization results of manual annotation and methods applied to the BRCA dataset. (b) Visualization results of manual annotation and methods applied to the MBA dataset. High-resolution images are available for viewing at https://github.com/bioszhr/AFSC/tree/ma... | [
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"caption": "Visualization results of datasets at spot resolution. Visualization results of manual annotation and methods applied to the BRCA dataset. High-resolution images are available for viewing at https://github.com/bios... | |
SEMITONES identifies spatially restricted markers from spatial transcriptomics data. (A) The spatially resolved expression profile of top spatially enriched SEMITONES genes. (B) The significance level in the number of standard deviations away from the mean of the empirical null distribution for a marker gene of fibre t... | [
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"caption": "SEMITONES identifies spatially restricted markers from spatial transcriptomics data. The annotation of spots as belonging to the fibre tracts, the glomerular layer of the main o... | |
The results of the PAGA algorithm on the hematopoiesis data of Paul et al. [2015] highlight strong connectivities between clusters 1–6. We use SlowMoMan to explore important features along a custom manifold between clusters 1–7. (a) The UMAP embedding of the hematopoiesis data of Paul et al. [2015] with the PAGA connec... | [
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"caption": "The results of the PAGA algorithm on the hematopoiesis data of Paul et al. [2015] highlight strong connectivities between clusters 1–6. We use SlowMoMan to explore important features ... | |
Single-cell spatial transcriptomics profiling by Molecular Cartography reveals dynamic zonation changes in EC-Wnt2-9b-DKO mice (A) UMAP plots of single-cell transcriptomic analysis of Molecular Cartography data showing genetic clusters of hepatocytes from control and EC-Wnt2-9b-DKO livers based on expression of 16 zona... | [
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"caption": "Single-cell spatial transcriptomics profiling by Molecular Cartography reveals dynamic zonation changes in EC-Wnt2-9b-DKO mice. Molecular Cartography depicting altered spatial expression of Ccnd1... | |
OTUD5 is a GPX4-interacting protein for stabilization in response to I/R. a PRTCs were induced by H/R in the presence or absence of the proteasome inhibitor MG132, or the lysosome inhibitor chloroquine (CQ) for 3 h. Cells were collected, and the protein levels were analyzed by immunoblotting. b Immunoblot and quantific... | [
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"caption": "OTUD5 is a GPX4-interacting protein for stabilization in response to I/R. Immunoblotting and quantification of GPX4 and OTUD5 expression in siOTUD5-infected HK2 cells, which were pretreat... | |
Application of TACIT on Xenium data. (a) UMAP and (b) spatial plots color-coded by identified cell types. The UMAP plots demonstrate TACIT’s ability to cluster cells accurately, showing a clear separation of different cell types. Epithelial such as mucous acinar, myoepithelial, and seromucous acinar cells form more dis... | [
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"caption": "Application of TACIT on Xenium data. UMAP plots with low granularity cell types across the three methods. TACIT’s enhanced capabilities are further exemplified by its identification of rar... | |
Spatial domain detection analysis results of the Human cortex data from DLPFC: (A) The detected spatial domains for Sample 151670: Annotated domain used as the ground truth (left), by SpatialPCA (middle), and by our framework (Right). (B) The t-SNE plot for all the SVGs detected by SPACE for Sample 151670. SVGs are col... | [
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"caption": "Spatial domain detection analysis results of the Human cortex data from DLPFC: Comparison of PAS score between SpatialPCA and our framework based on all 12 samples."
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Representative images of spatial domains discovered using CellTransformer and comparison to CCF. (a.) Four sequential tissue sections (note that the inter-section distance is roughly 200 µm) from anterior to posterior. In the first three columns, each dot is a cellular neighborhood colored by the cluster label when k-m... | [
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"caption": "Representative images of spatial domains discovered using CellTransformer and comparison to CCF. Same as c. but quantifying a maximum similarity of any given CellCharter or CellTransform... | |
RegulatoryCd138 plasma cells expand during chronic T. brucei infection. A UMAP plot of oligodendrocyte/B cell subclusters. B Heatmap of the top 50 most abundant genes in the subcluster in (A). C As in A but depicting the identified different time points. Dotted line represents clusters exclusively detected in infected ... | [
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"caption": "RegulatoryCd138 plasma cells expand during chronic T. brucei infection. Flow cytometry of CD138+ plasma cells and CD19+ B cells in naïve (n = 3 mice), the first peak of infection (7dpi; n... | |
Higher immune‐suppressive potential coupled with active dysfunction of T cells in cervical cancer compared to precancer: (A) the UMAP plot of T lymphocytes which could be further reclustered into CD8+ T cells and CD4+ T cells; (B) the UMAP plot of the CD8+ T cells reclustered into seven subsets, including CD8+ MAIT, CD... | [
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"caption": "Higher immune‐suppressive potential coupled with active dysfunction of T cells in cervical cancer compared to precancer: the violin plots indicating the naiveness score, cytotoxicity score and exhaustion ... | |
Molecular characterization of PtPM and RPM primary prostate tumor transplants demonstrates emergence of neuroendocrine carcinoma marker expression. a. Representative histological analysis of PtPM (top) and RPM (bottom) tumors isolated at 4-weeks post-transplantation. Serial sections depict immunohistochemical staining ... | [
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"caption": "Molecular characterization of PtPM and RPM primary prostate tumor transplants demonstrates emergence of neuroendocrine carcinoma marker expression. Heatmap depicting th... | |
BarDensr outperforms the existing methods by discovering more rolonies. (A) Performance of BarDensr on simulated data. What percentage of rolonies are correctly detected? We use the Receiver Operating Characteristic curve (ROC curve) to look at this percentage (the complement of False Negative Rates, or 1-FNR) as a fun... | [
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"caption": "BarDensr outperforms the existing methods by discovering more rolonies. Performance of BarDensr on simulated data. What percentage of rolonies are correctly detected? We use the Receiver Operating Characteristic curv... | |
Annotation of DAPI or HE areas differentiate myeloid and lymphoid transcript clusters in the human TB granuloma. Example of annotated regions of a section of human lung TB lesion. Areas were selected based on their density of DAPI (in green low density and in red high density). Decoded M4SA1 and CD68 sequences in the s... | [
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"caption": "Annotation of DAPI or HE areas differentiate myeloid and lymphoid transcript clusters in the human TB granuloma. The mean relative density of transcripts in lymphoid and myeloid regions in sections of pu... | |
Spatial analysis of T cell distribution in glioblastomas. a Illustration of the workflow using spatially resolved transcriptomics (stRNA-seq). b Histological images (H&E), upper plot, and surface plots of the gene set enrichment of the mesenchymal-like signature (n = 3 patients) c, d Spatial correlation analysis with M... | [
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"caption": "Spatial analysis of T cell distribution in glioblastomas. Spatial distance between tumor subtypes and exhausted CD8+ cells from IMC data."
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The impact of PGAM1 on the Tumor Immune MicroEnvironment (TIME) was investigated. Immunological analyses of immune infiltrates and immunosuppressants were carried out using GSE159115 and GSE121636 databases, respectively, as shown in (A). Furthermore, a heatmap was presented to depict the correlation between PGAM1 expr... | [
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"caption": "The impact of PGAM1 on the Tumor Immune MicroEnvironment (TIME) was investigated. Immunological analyses of immune infiltrates and immunosuppressants were carried out using GSE159115 and GSE121636 databases, respect... | |
Inpp5d/ SHIP1 knockdown increased amyloid pathology and
plaque-associated microglia number. A,
Inpp5dfl/fl/Cx3xr1CreER+
mice were crossed with the amyloid-depositing
APP/PSEN1
mouse model of Alzheimer’s disease (AD) to obtain either heterozygous
PSAPP mice, that is,
PSAPP/Inpp5dfl/fl/Cx3xr1CreER+
(PSAPP) or wild-type l... | [
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"caption": "Inpp5d/ SHIP1 knockdown increased amyloid pathology and plaque-associated microglia number. Inpp5dfl/fl/Cx3xr1CreER+ mice were crossed with the amyloid-depositing APP/PSEN1 mouse model o... | |
Subsets analysis and MIA mapping of epithelial cell ( Identification of subgroups of epithelial cells in ESCC. b. The distribution of epithelial cells in three ESCC patients. c. Characteristic gene expression heatmap of each subgroup of epithelial cell. d. Cell number and sample proportion of each cell subsets. e. MIA ... | [
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"caption": "Subsets analysis and MIA mapping of epithelial cell (Identification of subgroups of epithelial cells in ESCC. MIA results of epithelial cells in cancer and stroma of spatial transcript... | |
Sex differences within the AD in DS cohort. a, We performed differential expression analyses between female and male samples for each spatial cluster within the AD in DS cohort for our ST dataset. Since we had more female than male samples in the ST dataset, we subsampled the ST spots in the female samples to match the... | [
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"caption": "Sex differences within AD in DS cohort. We performed differential expression analyses between female and male samples for each spatial cluster within the AD in DS cohort for... | |
ADEPT improves spatial domain identification, enhances the spatial patterns of layer-marker genes, and correctly infers the spatial trajectory on DLPFC section 151675 (A) Best clustering results from six tools. Each visualization result has seven different clusters, corresponding to six different cortical layers and wh... | [
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"caption": "ADEPT improves spatial domain identification, enhances the spatial patterns of layer-marker genes, and correctly infers the spatial trajectory on DLPFC section 151675. UMAP visualizations, an... | |
Effector CD8+T cell subset identification in the PCa microenvironment. A) Unsupervised clustering of T cells gave rise to 7 sub‐clusters. B–D) Comprehensive B) utilize feature plot, C) violin plot, and D) dot plot to illustrate the marker genes expression pattern in CD4T (CD4), CD8T (CD8ACD8B), γδT (CD4‐CD8) as well as... | [
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"caption": "Effector CD8+T cell subset identification in the PCa microenvironment. Comprehensive dot plot to illustrate the marker genes expression pattern in CD4T (CD4), CD8T (CD8ACD8B), γδT (CD... | |
Characterize the heterogeneity of fibroblast subpopulations. A) scRNA‐seq of PCa fibroblasts revealed five distinct cell types based on their transcriptional profiles. B–D) Comprehensive utilized B) violin plot, C) feature plot, and D) dot plot to illustrate their marker genes expression pattern among the 5 distinct fi... | [
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"caption": "Characterize the heterogeneity of fibroblast subpopulations. In situ analysis of FOXP3+ regulatory T cells and FAP+ fibroblasts in the malignant PCa patients. The line plot indic... | |
Comparative performance of SpaCAE to existing spatial and non-spatial methods on spatial domain identification. (A) DLPFC layers were annotated by Maynard et al. The ground truth of spots was mapped on their spatial position in slide 151675 (n = 3592 spots), which was separated into six cortical layers (L1–L6) and WM. ... | [
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"caption": "Comparative performance of SpaCAE to existing spatial and non-spatial methods on spatial domain identification. ARI boxplots of whether deep spatial contrast is used, whether spatial data augme... | |
Reanalysis of B cell subset. (A) UMAP of B cell subset. (B) Expression of selected genes in B cell subset. (C) Expression of immunoglobulin genes in B cell subset. | [
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"caption": "Reanalysis of B cell subset. Expressi... | |
STAMP deconvolutes CAFs from regular fibroblasts in SMI NSCLC data. a, NSCLC sample data acquired using CosMx Spatial Molecular Imager (SMI) with the original cell type annotation. b, Gene module rankings (number) and scores (color) of marker genes for each topic. c, Spatial plots of topics annotated using their gene m... | [
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"caption": "STAMP deconvolutes CAFs from regular fibroblasts in SMI NSCLC data. Gene module rankings (number) and scores (color) of marker genes for each topic."
},
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... | |
Systematic parameter optimization and integration of DeepST. (A) The ARI pirate graph of nine GNN types, each of which was evaluated on 12 DLPFC slides, respectively. Spatial domain distributions of slides 151673 and 151507 with various networks (SGCConv, ResGatedGraphConv and GCNConv) are displayed, respectively. (B) ... | [
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"caption": "Systematic parameter optimization and integration of DeepST. The ARI pirate graph of nine GNN types, each of which was evaluated on 12 DLPFC slides, respectively. Spatial domain distributions of slides 151673 a... | |
Spatial transcriptome analysis of E13.5 limb tip (ROI_A). (a) Volcano plots of DEGs up-regulated and down-regulated in the MO embryonic limb tip compared with those in the CT group. (b) Down-regulated migration-related GO biological process terms in the limb tip of the MO embryo compared with the CT group. (c). Down-re... | [
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"caption": "Spatial transcriptome analysis of E13.5 limb tip (ROI_A). Volcano plots of DEGs up-regulated and down-regulated in the MO embryonic limb tip compared with those in the CT group.... | |
Spatially driven signaling in melanoma LMD. A. Schematic showing the basic principles behind the algorithm used to identify KEGG pathway enrichment that have significant spatial patterns (left) and a heatmap highlighting the quantity and similarities/differences of KEGG pathways showing significant spatial pattern with... | [
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"caption": "Spatially driven signaling in melanoma LMD. Schematic showing the basic principles behind the algorithm used to identify KEGG pathway enrichment that have significant ... | |
Overlap in β-cells with high PFKFB3 and MAIP1 expression. (A, B, C) Representative immunofluorescence images of islets from mice as described in Fig 5, double immunostained for insulin and MAIP1 (red), insulin (green), and nuclei (blue). The sectioning was performed across the whole pancreas. For quantification of MAIP... | [
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"caption": "Overlap in β-cells with high PFKFB3 and MAIP1 expression. Represe... | |
Spatiotemporal analysis of key biological processes during barley germination. (A) Tissue specific functional category analysis. The categories identified from wordcloud outputs for the gene lists at each time point and tissue are shown, for those categories identified in at least three time points for a given tissue t... | [
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"caption": "Spatiotemporal analysis of key biological processes during barley germination. Most highly expressed genes across all samples. The table shows the genes expressed in 15 or more of the 25 samples makin... | |
Indicators of OXPHOS and glutathione biosynthesis in HltfCDX model. (A) Photomicrograph emphasizes gradient of positive immunostaining for MT-CYB in tumor cells of the HltfCDX including tumor cells in lymphatic intravascular niches (blue arrow heads) of the mouse TME. 10X magnification. (B) Violin plots from spatial tr... | [
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"caption": "Indicators of OXPHOS and glutathione biosynthesis in HltfCDX model. Violin plots from spatial transcriptomics depicts regional gene expression. Each violin plot is a composite of genes. The top ... | |
Processing whole_mouse_embryo data on MULTILAYER (A) When the size matrix defined by the user doesn’t comply with the grid size retrieved within the data, a size warning error is displayed. User can decide whether or not to accept the proposed grid size modification. This option does not impact the computing steps, but... | [
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"caption": "Processing whole_mouse_embryo data on MULTILAYER. As MULTILAYER processes the data, the Anaconda prompt interface displays a listing of the different steps taking place."
},
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"bbox": [... | |
VCAM-1 mediates inflammation by enhancing mtDNA synthesis. (A-D) mtDNA levels by qPCR after oxLDL treatment (A, normalized to nLDL, n = 4/group, two-tailed t-test), mtDNA synthesis gene expression after nLDL (n) or oxLDL(ox) treatment by qPCR (B), and representative 8-OHdG, EdU, and TOM20 images after oxLDL treatment (... | [
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"caption": "VCAM-1 mediates inflammation by enhancing mtDNA synthesis. Polg, Cmpk2 and Pgc1a were silenced selectively in macrophages of female Ldlr−/− mice on atherogenic diet by siRNA delivery in DOTAP l... | |
Functional study of ZmSUT genes in maize seed. a Spatial expression patterns of ZmSUT (14 DAP) and Betl9 (14 and 18 DAP) genes. b Semi-thin sections (panels 1 and 2) and transmission electron microscopy (TEM, panels 3 and 4) of the BETL region in the wild-type KN5585 (panels 1 and 3) and zmsutRNAi-1/7 (panels 2 and 4) ... | [
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"caption": "Functional study of ZmSUT genes in maize seed. Plant phenotypes of the wild-type KN5585, selfing zmsut1/7RNAi-1, selfing zmsut1/7RNAi-2, WT × RNAi-1 and WT × RNAi-2. Bar = 10 cm."
},
... | |
Prediction of cancer cells. (A) Heatmap of the predicted cancer cells. The upper markers are chromosomes 1 to 22 and X. The color markers on the left represent the predicted cell types, where green are normal cells and red are predicted cancer cells. Blue in the heat map indicates loss and red indicates amplification; ... | [
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"label": "B",
"caption": "Prediction of cancer cells. Cell types used for CopyKAT analysis."
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DeST-OT analysis of axolotl brain development. a, Stereo-seq data from axolotl brain sections at embryonic stage 44, embryonic stage 54, embryonic stage 57, Juvenile stage, and Adult stage, with cell type labels from [43] b, Cell type transition graph derived from DeST-OT alignments throughout axolotl brain development... | [
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"caption": "DeST-OT analysis of axolotl brain development. Cell type transition graph derived from DeST-OT alignments throughout axolotl brain development. The cell types are arranged in a half circle. A cell... | |
Robust signatures of granulosa and theca cells. (A) Focused PCA of the 5 theca-enriched ROIs and 11 granulosa-enriched ROIs from donor 1, showing their separation into two clusters. (B) Similar PC plot for 6 theca and 18 granulosa ROI samples from donor 2. (C) Expression specificity of the 94 granulosa cell maker genes... | [
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"caption": "Robust signatures of granulosa and theca cells. Similar PC plot for 6 theca and 18 granulosa ROI samples from donor 2."
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Spatial transcriptomics clustering and marker genes of four pancreatic tissues at different locations. (A) Normal pancreas tissue (NP, green circle) and pancreatic ductal adenocarcinoma tissues, including tumor (T, yellow circle), tumor stroma (TS, red circle), and adjacent tumor tissue (ATT, blue circle), were selecte... | [
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"caption": "Spatial transcriptomics clustering and marker genes of four pancreatic tissues at different locations. Normal pancreas tissue (NP, green circle) and pancreatic duct... | |
Identification of astrocyte transcriptomic gene modules. (A) Heatmap showing pairwise correlations of non-negative matrix factorization (NMF) submodules derived from 294 samples. The resembled submodules across samples are aggregated into 7 modules (M1−M7). (B) Heatmap showing expression of marker genes within each mod... | [
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"caption": "Identification of astrocyte transcriptomic gene modules. The interaction networks for the M2 ECM and M4 stress modular genes (blue, M2 modular genes; red, M4 modular genes). Node size i... | |
Comparative spatial transcriptomics of nematodes. (a, b) The schematics represent anatomical overviews of Pristionchus pacificus (a) and Caenorhabditis elegans (b) hermaphrodites together with expression domains of selected marker genes which were used to define regions across the A–P axis. For example, P5 was defined ... | [
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"caption": "Comparative spatial transcriptomics of nematodes. Hierarchical clustering of P. pacificus sections based on Pearson correlation indicates that sections within a region are generally highly simil... | |
Single nucleus RNA sequencing of mPFC from 2BC-CIE paradigm treated animals: (a) Schematic diagram showing the experimental design, animals were subjected to chronic intermittent ethanol or air (control) followed by 2 h 2 bottle choice (ethanol/water), after 5 CIE sessions, brains were collected, flash frozen, mounted ... | [
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"caption": "Single nucleus RNA sequencing of mPFC from 2BC-CIE paradigm treated animals: tSNE plot showing single nuclei clustering from alcohol vapor and air control samples, color coded by ... | |
Protein markers of murine CD45− cell subsets, related to Figure 3 (A) CITE-seq data from the murine CD45− cells in Figure 3A were exported as an FCS file and an in silico gating strategy identified in FlowJo. (B) Gated cell overlay of populations identified using strategy in (A). (C) Expression of CD90, CD204, CD73, an... | [
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"caption": "Protein markers of murine CD45− cell subsets, related to Figure 3. Expression of indicated protein markers in 60-plex MICS analysis in endothelial cells. PV, portal vein; CV, central v... | |
Collecting and classifying bulk transcriptomes of nephron progenitor niches from three branching life-cycle stages. (A) Top, Schematic of E17 kidney flattening, sectioning and processing for GeoMx spatial sequencing. Transcripts from cap mesenchyme cells in 47 individual regions of interest (ROIs) were collected and se... | [
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"caption": "Collecting and classifying bulk transcriptomes of nephron progenitor niches from three branching life-cycle stages. Plots of median gene expression vs. GeoMx ... | |
ST analyses demonstrate decreased presence of early RPCs in the ciliary margin zone as development proceeds from 10 to 13 PCW. A–C Spatial localisation of all cell clusters identified from the ST analyses. Four sections from each eye sample were processed for ST analyses. D The CMZ clusters are shown for each developme... | [
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"caption": "ST analyses demonstrate decreased presence of early RPCs in the ciliary margin zone as development proceeds from 10 to 13 PCW. Spatial localisation of all cell clusters identified from the ST analyses. Four sections... | |
DEGs in Glial Cells Overall and Among Different Clusters. A Heatmap representation of the top 20 differentially expressed mRNAs in glial cells between TLE and control hippocampi. B Representative volcano plot showing the major DEGs in glial cells between TLE and control hippocampi. C GO enrichment analysis of the major... | [
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"caption": "DEGs in Glial Cells Overall and Among Different Clusters. GSEA analysis results for genes with elevated expression in glial cells of TLE group."
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Heterogeneity analysis of the three DTLH clusters located in different renal medullary regions. a The spatial location of the SSBpr/ErprT and SSBmd/DTLH clusters. The green color represents the SSBpr/ErprT cluster (outer layer of the medulla), the red color indicates the SSBmd/DTLHa cluster (the middle layer of the med... | [
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"caption": "Heterogeneity analysis of the three DTLH clusters located in different renal medullary regions. Heatmap illustrating the genes encoding complex subunits of mitochondrial OXPHOS, gradually increasing from outer... | |
Cell–cell interactions. The interactions among 29 cell types in the (A) HCC group and (B) HCC-SDS group. (C) Frequency of interaction between cancer cells and CAFs. (D) Frequency of interaction between cancer cells and T cells. (E) Incoming and outgoing interaction strength between cancer cells and CAFs. (F) Heatmap of... | [
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"caption": "Cell–cell interactions. The interactions among 29 cell types in the HCC group."
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"caption": "Cell... | |
The model’s performance is constructed on the data without feature selection, which is called the “original model” in the following part. (A,C): The receiver operating characteristic curve (ROC) of training and independent test original model constructed using the sample collected from the patients who have received im... | [
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"caption": "The model’s performance is constructed on the data without feature selection, which is called the “original model” in the following part. The receiver operating characteristic curve (ROC) ... | |
Comparison between RRST and standard Visium on an adult human small intestine sample over time. a Representative H&E image (top) and spots colored by five major tissue regions (bottom): mucosa, TLS, submucosa, muscularis, and serosa. TLS, Tertiary Lymphoid Tissue. The full small intestine dataset consisted of 14 tissue... | [
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"caption": "Comparison between RRST and standard Visium on an adult human small intestine sample over time. Overview of data quality in the five annotated tissue regions over time, visualized by violin plot... | |
STRING analysis of DEGs between SNc and VTA identifies novel networks for the two midbrain dopamine neuron subpopulations. The two STRING networks are based on 23 DE genes highly expressed in SNc (A) and 51 DE genes highly expressed in VTA (B). Different color edges represent the interactions by curated databases, expe... | [
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"caption": "STRING analysis of DEGs between SNc and VTA identifies novel networks for the two midbrain dopamine neuron subpopulations. The two STRING networks are based on 23 DE genes highly expressed in SNc. Dif... | |
Spatial and transcriptional properties of inflammatory clusters. (A) Representative spatial feature plots of naïve (top row) and experimental autoimmune encephalomyelitis (EAE) (bottom row) samples colored by cluster show consistent labeling of anatomic regions and the distribution of meningeal inflammation (cluster 11... | [
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"caption": "Spatial and transcriptional properties of inflammatory clusters. Representative images of gadolinium-enhanced magnetic resonance imaging (MRI) scans collected 10 weeks after... | |
Enhancing spatial transcriptomics data with scRNA-seq data. This analysis step augments ST data using scRNA-seq data. a By using scRNA-seq data onto the spatial dataset, the composition of individual spots can be understood in terms of single cells, such as by computing enrichment scores, which measure the expression o... | [
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"caption": "Enhancing spatial transcriptomics data with scRNA-seq data. This analysis step augments ST data using scRNA-seq data. scRNA-seq data can be used to increase resolution of multi-cell ST data, by mappi... | |
High-dimensional characterization of metabolic alterations in myocardial infarction by spatial trajectories and multimodal Raman-MALDI imaging. a H&E Staining of a murine sagittal heart section after induction of myocardial infarction by transient ligature of the LAD. Dashed box denotes cardiac tissue with transition f... | [
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"caption": "High-dimensional characterization of metabolic alterations in myocardial infarction by spatial trajectories and multimodal Raman-MALDI imaging. Volcano plot of n = 3 individual hearts explo... | |
Genes are expressed differently in various cancer clones. The expression of the 30 genes that were inferred by the regression model as the most active in at least one clone, clustered in rows and columns, for breast (a) and prostate cancer (b) tissues. * cancer gene found in all cancer tissues (not cancer type specific... | [
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"caption": "Genes are expressed differently in various cancer clones. The expression of the 30 genes that were inferred by the regression model as the most active in at least one clone, clustered in rows and columns, for breast canc... | |
Venous-resident Pdcd10-ko endothelial progenitor cells support the formation of cavernomas. (A) Expression levels of Bst1 as measured according to Visium Spatial Transcriptomics. All of the sequenced dots are shown, color coded for expression, as blue, low; red, high. Negative spot outlines are shown without any fill c... | [
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"caption": "Venous-resident Pdcd10-ko endothelial progenitor cells support the formation of cavernomas. Expression levels of representative lesion markers (as indicated) from Visium analysis. For... | |
Schematic overview of spaCI. (A) The spaCI method leverages the spatial relationships between cells as well as the expression data of all available genes to infer the L–R interactions. (B) In spaCI, genes are projected into the latent space through two components: a gene-based linear encoder as well as a cell-based att... | [
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"caption": "Schematic overview of spaCI. The spaCI method leverages the spatial relationships between cells as well as the expression data of all available genes to infer the L–R interactions."
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(A) UMAP dimensionality reduction visualization of colitis status or tissue type information, based on pixel level N-glycan signals from MALDI-MSI. Pixels were either colored by colitis status or tissue location. (B) Representative images of selected N-glycan signals from small and large intestinal tissues. A total num... | [
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"caption": "Heatmap of the average N-glycan level for each pixel level cluster from pixie."
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MIST outperforms other imputation methods in holdout experiments. a–b Dot plots of (a) rooted mean square error (RMSE) and (b) Pearson’s correlation coefficient (PCC) in the fivefold holdout experiment using multiple datasets. Each column on the X axis is an individual dataset (Supp. Table 1). Colors of dots represent ... | [
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"caption": "MIST outperforms other imputation methods in holdout experiments. The Spearman’s rank correlation coefficient (r) between holdout input and observed GAPDH expression values."
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GO cluster network enrichment among the genes. Enrichment among genes with (A) de novo and (B) recessive damaging variants in Chinese and PCGC EU TOF trios. Color of the nodes reflects the strongest enrichment among the Chinese only (red), European only (blue) or combined (mixed) analyses. Top GO terms of selected clus... | [
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"caption": "GO cluster network enrichment among the genes. Enrichment among genes with recessive damaging variants in Chinese and PCGC EU TOF trios. Color of the nodes reflects the strongest enrichment a... | |
ADTD recovers cellular regulation and retains prediction performance in the breast cancer test scenario. The left Figure shows ROC AUCs for recovering cellular regulation simulated in all cell types for different regularization parameters λ2 and fixed value for ADTD in the breast cancer test study. The corresponding p... | [
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"caption": "ADTD recovers cellular regulation and retains prediction performance in the breast cancer test scenario. The corresponding performance in terms of Pearson’s correlation for ADTD for estimating ... | |
Region-dependent transcriptional dynamics of human CNS border macrophages during development. a, Schematic overview of the included time points and compartments color coded for the studies from which immune-cell data were integrated with the present data. b, UMAP visualization of single-nucleus RNA-seq data from 59,053... | [
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"caption": "Region-dependent transcriptional dynamics of human CNS border macrophages during development. Schematic overview of the included time points and compartments color coded for the studies from which imm... | |
Microglial impairments in SZ. a
Post-mortem studies report changes in microglial density [52, 89, 197], arborization and gene expression [80, 139, 156, 176, 222] in patients with SZ compared to controls. TSPO-PET shows conflicting findings, however, there is a suggestion of decreased TSPO binding in grey matter in pati... | [
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"caption": "Microglial impairments in SZ. Drawing of 3D microglial morphology in a control brain (left) and a schizophrenia brain (right). Images adapted and redrawn from De Picker et al. [31]'s origin... | |
Results of applying RegionalST to two breast cancer spatial transcriptomics datasets and an ovarian cancer dataset. (A) Weighted entropy of the tumor slide based on the spatial transcriptomics data. (B) ROIs in the first breast cancer data using a radius size of 15. The detailed cell type labels associated with (B) are... | [
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"caption": "Results of applying RegionalST to two breast cancer spatial transcriptomics datasets and an ovarian cancer dataset. Barplot of the DEG numbers with adjusted P value smaller than 0.05 in different cells ty... | |
Generating expression based tree classifiers to identify hypoxic samples. A Decision trees generation overview. 425 RNA-seq samples exposed to normoxia or hypoxia were processed to produce a ranking set of genes from each of one them. A subset of the resulting data matrix, consisting in the 178 genes significantly up-r... | [
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"caption": "Generating expression based tree classifiers to identify hypoxic samples. Mean decrease in accuracy index of the 20 most important genes according to 1000 random forest iterations."
},... | |
Expression of the top 3 most differentially expressed genes across human DRG neuronal subclusters. (A, B) Dot plot (A) and heatmap (B) showing the expression of the top three most differentially expressed genes across human DRG neuronal subclusters. DRG, dorsal root ganglia. | [
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"caption": "Expression of the top 3 most differentially expressed genes across human DRG neuronal subclusters. Dot plot showing the expression of the top three most differentially expressed genes across human DRG neuronal subclu... | |
Spatial domain annotation in the DLPFC 10x Visium dataset. (A) Boxplots of Kappa, mF1, and ACC showing the accuracy of different methods for domain annotation across 12 tissue sections. (B) Spatial domain annotation in tissue sample ID151673 for ground truth, SpatialAnno, scSorter, SCINA, Garnett and CellAssign. (C) To... | [
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"caption": "Spatial domain annotation in the DLPFC 10x Visium dataset. Boxplots of Kappa, mF1, and ACC showing the accuracy of different methods for domain annotation across 12 tissue sections."
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β-catenin and 11p15.5 locus oncogenic cooperation in mosaic and non-mosaic HB tumors. a Evolution of β-catenin and 11p15.5 locus alteration spectra with age at surgery in 74 and 72 patients, respectively. One sample per patient was represented. A two-sided χ² test was performed. b Heatmap representation of CTNNB1 and 1... | [
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"caption": "β-catenin and 11p15.5 locus oncogenic cooperation in mosaic and non-mosaic HB tumors. First Kaplan–Meier curve indicates progression-free survival in mosaic (n = 12) and non-mosaic pa... | |
Interneuron taxonomy is consistent across multiple human striatal snRNA-seq datasets. A (left) UMAP of interneuron nuclei from five different datasets before and (middle) after integration with scVI. (right) Barplot indicating the total number of nuclei from each dataset. B UMAP of the integrated data colored by cluste... | [
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"caption": "Interneuron taxonomy is consistent across multiple human striatal snRNA-seq datasets. UMAP of interneuron nuclei from five different datasets before and after integration with... | |
Tumour immune microenvironment in CM dissected at a single‐cell resolution. (A) The UMAP plot showing subclusters of lymphoid cells. The small panel shows cells color‐coded by the cell type. (B) The dot plot showing the expression of marker genes for each subcluster of lymphoid cells. (C) Relative proportion of each su... | [
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"caption": "Tumour immune microenvironment in CM dissected at a single‐cell resolution. The UMAP plot showing subclusters of myeloid cells. The small panel shows cells color‐coded by cell type. CM, cardiac ... | |
Effect of ADM knockout in trophoblast differentiation into SCT and EVT. (A) ADM guide RNAs (gRNAs) for CRISPR-Cas9–mediated knockout of the human ADM gene. (B) Expressions of ADM were analyzed by Western blotting, with α-tubulin used as the internal control. N = 5. (C) Bright-field images of control TSC/TSCADM KO diffe... | [
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"caption": "Effect of ADM knockout in trophoblast differentiation into SCT and EVT. Expressions of ADM were analyzed by Western blotting, with α-tubulin used as the internal contr... | |
Workflow of EAGS. (A) Data generation process for the input of EAGS. (B) The EAGS method calculates the nearest-neighbor information based on the gene expression pattern and spatial information. Then, EAGS adaptively generates smoothing weights and outputs the smoothed results. | [
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"caption": "Workflow of EAGS. The EAGS method calculates the nearest-neighbor information based on the gene expression pattern and spatial information. Then, EAGS adaptively generates smoothing weights and outputs th... | |
Reduced microglial and astrocytic response to tau induced by ApoeCh. a, c Representative confocal images of immunostained dentate gyrus for GFAP (blue, a) and IBA1 (red, c) of 9-mo-old WT, ApoeCh, PS19, and PS19;ApoeCh mice. Scale bar=100μm. b,d Quantification of total volume of GFAP+ cells (b) and IBA1+ cells (d). n=4... | [
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"caption": "Reduced microglial and astrocytic response to tau induced by ApoeCh. Cell types plotted in XY space."
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The LSGI framework and downstream analysis. A. Demonstrative plot showing existence of cell phenotypic gradient, summarized by some molecular programs, on a spatial map of tissue. Dark blue color demonstrates higher activity levels of the molecular program. Arrows indicate the direction of gradients. B. LSGI employs NM... | [
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"caption": "The LSGI framework and downstream analysis. LSGI partitions cells into small groups based on their spatial localizations. One cell can be assigned to multiple groups."
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Distinct ME astrocyte subtypes observed with unique interactions with blood vessels. a, UMAP plot of 8,508 astrocyte transcriptomes. Astrocyte subtypes were identified with an unbiased analysis. The number of each cell subtype profiled is indicated in the plot legend. b, Violin plot showing the expression level of a su... | [
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"caption": "Distinct ME astrocyte subtypes observed with unique interactions with blood vessels. Tomato in the cortex and ME of Slco1c1-CreER:Ai14 mice. Tomato (red) indicates Slco1c1 expression.... | |
Validation of NS-Forest minimal markers and assessment of the top NS-forest markers. a,b, Annotated UMAP plots following data integration using either the minimal marker genes (left) or the equivalent number of a random set of genes (right) as anchors for the adult (a) and paediatric (b) datasets. The colour scheme for... | [
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"caption": "Validation of NS-Forest minimal markers and assessment of the top NS-forest markers. Annotated UMAP plots following data integration using the minimal marker genes as anchors for the paediatric dataset... | |
SHM-seq accurately captures bacterial representation and abundances in SPF and ASF mice. a, Bacterial reference of the mouse gut microbiome. Phylogenetic tree of SPF colonic content, representing the 65 species colored to highlight taxonomic families and genera. b, Enhanced annotation performance of the deep learning m... | [
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"caption": "SHM-seq accurately captures bacterial representation and abundances in SPF and ASF mice. SHM-seq agreement with FISH probes targeting ASF502. Cross-section of an ASF mouse colon (scale bar, 180... | |
Evaluating gene panels based on their ability to reconstruct scRNA-seq expression profiles. The selected genes are used to predict either log-normalized expression counts for the remaining genes (A, C, E) or whether each gene is expressed in the genome-wide profile (B, D, F). The panels selected by PERSIST perform bett... | [
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"caption": "Evaluating gene panels based on their ability to reconstruct scRNA-seq expression profiles. The selected genes are used to predict log-normalized expression counts for the remaining genes. The panels selected by... | |
Expression of epithelial gene markers in the skin. a) Avg. Log2 expression of all epithelial gene markers listed in Supplementary File 1, for the skin, operculum, caudal fin, and pectoral fin. Magnified areas of each section are in the upper right corner, and area of magnification is marked by circles on the main slide... | [
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"caption": "Expression of epithelial gene markers in the skin. Avg. Log2 expression of all epithelial gene markers listed in Supplementary File 1, for the skin, operculum, caudal fin, and pectoral fin. Magnified ... | |
Heterogeneity of cancer cell EMT, proliferation, and senescence revealed by DSP transcriptomics. (A) Representative immunofluorescent staining indicating heterogeneous PanCK expression in Tumor-ROIs: HighCK (up) and LowCK (down). (B) Violin plots of EMT scores based on RNA count across all tumor ROIs by the patient. (C... | [
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"caption": "Heterogeneity of cancer cell EMT, proliferation, and senescence revealed by DSP transcriptomics. Comparison of EMT scores between Tumor-ROIs with and without necrosis in Patient 3. **** P < 0.0... | |
Cellular disruption and tissue identity loss from SARS-CoV-2 infection (A) Specific gene expression distributions for cardiomyocyte-related genes (from patient autopsy samples, n = 41). (B) Sample collection strategy for COVID-19 autopsy samples from complete adult cases. (A–J) Two cases with representative hematoxylin... | [
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Comparative analysis of primary and organoid samples. A, UMAP representation of approximately 200,000 cells (∼48,000 cells from tumor PDOs with matched normal PDOs, combined with primary samples; ∼152,000 cells) recapitulating the major five metaclusters color-coded by their cell types. Each dot in the UMAP represents ... | [
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"caption": "Comparative analysis of primary and organoid samples. Volcano plot of upregulated and downregulated genes in the plasma metacluster between PDOs and primary samples, showing si... | |
SDUCL for dissecting heterogeneity in different tumors. (A) Histological images and manual annotations of the PDAC dataset. (B) Histological images and manual annotations of the BRCA dataset. (C) Clustering results on PDAC dataset. (D) Clustering results on BRCA dataset. (E) Volcano plots illustrating differentially ex... | [
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"label": "A",
"caption": "SDUCL for dissecting heterogeneity in different tumors. Histological images and manual annotations of the PDAC dataset."
},
{
"bbox": [
3.0399999999999983,
737.9... | |
Meningeal cells promote growth and resistance to MAPKi in vivo. A. A schematic outlining the experimental cohorts of the animal experiment. Mice were injected subcutaneously with 1 million WM164 cells alone, 1 million WM164 cells with 1 million primary meningeal cells (MC), or 1 million WM164 cells with 1 million derma... | [
{
"bbox": [
0,
137.01600000000002,
337.008,
326.01599999999996
],
"label": "B",
"caption": "Meningeal cells promote growth and resistance to MAPKi in vivo. Line graph showing the average growth of tumors in each experimental cohort over time, with error bars depicting standar... | |
Inhibitory neuronal subpopulations identified by secondary unsupervised clustering on inhibitory neurons in snRNA-seq data. We applied a secondary round of unsupervised clustering to the inhibitory neuron nuclei identified in the first round of clustering. This identified 14 clusters representing inhibitory neuronal su... | [
{
"bbox": [
370.0224,
0,
397.9776,
230.0048
],
"label": "B",
"caption": "Inhibitory neuronal subpopulations identified by secondary unsupervised clustering on inhibitory neurons in snRNA-seq data. We applied a secondary round of unsupervised clustering to the inhibitory neuro... | |
HOPX is a potentially novel DZ factor. (A) HOPX expression (normalized counts) in the human developing adrenal gland (combined adrenal gland samples, bulk RNA-Seq, n = 32) compared with controls (n = 14). (B) Feature plot of HOPX expression in the adrenal cortex clusters (for annotation, see Figure 1G). (C) Spatial tra... | [
{
"bbox": [
361.0269,
382.96529999999996,
206.0162,
165.996
],
"label": "G",
"caption": "HOPX is a potentially novel DZ factor. UMAP of key cortex clusters at 19wpc."
},
{
"bbox": [
17.027399999999997,
1.0178999999999965,
220.97270000000003,
18... | |
Bioinformatic validation of the clinical significance of ALKBH1 across multiple cancer types. The clinical significance of ALKBH1 from a pan-cancer perspective. Expression levels of ALKBH1 in various cancers and comparison between tumor and normal tissues with statistical significance denoted by asterisks (A). Kaplan–M... | [
{
"bbox": [
521.9875920000001,
365.01719999999995,
130.17300799999998,
127.9828
],
"label": "F",
"caption": "Bioinformatic validation of the clinical significance of ALKBH1 across multiple cancer types. The clinical significance of ALKBH1 from a pan-cancer perspective. Kaplan... | |
Overview of the study organisms and methods. a
Euroleon nostras larva in its natural habitat. Photo: Benjamin Weiss. b
Chrysoperla carnea larva in its natural habitat. Photo: Devasena Thiagarajan. c Schematic overview of the experimental approach. We combined transcriptomic, proteomic, and morphological analysis, inclu... | [
{
"bbox": [
355.0221,
0,
342.02070000000003,
225.0267
],
"label": "B",
"caption": "Overview of the study organisms and methods. Chrysoperla carnea larva in its natural habitat. Photo: Devasena Thiagarajan."
},
{
"bbox": [
3.0057000000000182,
0,
346.0... | |
Results of functional enrichment analysis and the correlation between tumor-specific T cell signature and immunotherapy-related genes. (A) GSEA results of activation of immune response pathways in the TstcSig-high vs. TstcSig-low group in the MIvigor210 cohort. (B) GSEA results of T cell acitivation involved in immune ... | [
{
"bbox": [
0,
0,
304.99710000000005,
298.0009
],
"label": "A",
"caption": "Results of functional enrichment analysis and the correlation between tumor-specific T cell signature and immunotherapy-related genes. GSEA results of activation of immune response pathways in the Tst... | |
Endothelial cell clusters. (A) Uniform manifold approximation and projection (UMAP) plot of 3,736 endothelial cells, color-coded by their corresponding patient (left) or associated cluster (right). (B) UMAP plot color-coded for expression (blue to gray) of marker genes for blood and lymphatic endothelial cells. (C) Vio... | [
{
"bbox": [
0,
180.0198,
321.9731,
328.005
],
"label": "C",
"caption": "Endothelial cell clusters. Violin plots of selected genes involved in angiogenesis."
},
{
"bbox": [
0,
509.0238,
246.02419999999998,
155.97719999999998
],
"label": ... |
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