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Cell type marker genes

Cell type differential genes

Spatial single gene pattern

Spatially patterned single genes

Spatial pattern pathways

spatially patterned Pathways

Cell-cell interactions using single cell data

scRNA-seq cell-cell interactions

Cell-cell interactions using deconvoluted spatial data

Cell-cell interactions using deconvoluted spatial data

Gene regulatory network analysis

Gene regulatory network analysis

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Title

PMID

Data

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region
30385464
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A spatially resolved brain region- and cell typespecific isoform atlas of the postnatal mouse brain
33469025 
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Cell2location maps fine-grained cell types in spatial transcriptomics
35027729
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Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease
32702314
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Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease
33083725
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Spatial organization of the somatosensory cortex revealed by osmFISH
30377364
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Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
33558695 
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Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
30948552
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Neuroinflammatory astrocyte subtypes in the mouse brain
34413515
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Molecular atlas of the adult mouse brain
32637622 
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Spatial transcriptome data from coronal mouse brain sections after striatal injection of heme and heme-hemopexin
35141374
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Molecular architecture of the developing mouse brain
34321664
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Embryo-scale, single-cell spatial transcriptomics
34210887
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High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue
33188776
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Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
34489600
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Integration of spatial and single-cell transcriptomics localizes epithelial cell–immune cross-talk in kidney injury
34003797
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Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model
33188776
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A coordinated progression of progenitor cell states initiates urinary tract development
33976190
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Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
29925878
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An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer
34385456
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Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity
34792289
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Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver
34857782
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
35021063
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Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level
34417225
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Spatiotemporal analysis of human intestinal development at single-cell resolution
33406409
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The spatial transcriptomic landscape of the healing mouse intestine following damage
35149721
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Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas
31932730
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Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
34857954
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Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
34650042
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A single-cell and spatially resolved atlas of human breast cancers
34493872
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Dissecting mammalian spermatogenesis using spatial transcriptomics
34731600
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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
31835037
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Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis
33741943
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Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface
34725363
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Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
32579974
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Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma
30154148
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Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation
preprint
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Spatial CRISPR genomics identifies regulators of the tumor microenvironment
35290801
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Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
35210624
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Human distal lung maps and lineage hierarchies reveal a bipotent progenitor
35355018
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T-cell dysfunction in the glioblastoma microenvironment is mediated by myeloid cells releasing interleukin-10
35177622
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Mapping the developing human immune system across organs
35549310
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Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
35512705
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