Topic 148

rna sequencing single heterogeneity scrna seq epithelial cell cells types tissue subsets transcriptomics immune tissues transcriptional cellular transcriptomic profiling distinct macrophages atlas signatures expression mesenchymal myeloid populations subtypes reveals subpopulations transcriptomes microenvironment cancer monocytes spatial spatially lung transcriptome samples biology define tumor markers mouse identified programs stromal resident profiles identify fibroblasts clusters macrophage gene diversity signature revealed progression analysis genomics human composition inflammatory ligand epithelium compartment endothelial identifies homeostasis tumors clustering genes disease phenotypes resolution landscape dendritic fibroblast cluster tumour organoids stem transcripts states biopsy matrix goblet sections limited pericytes expressing enriched patient subtype including map infiltrating molecular profile interactions

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Definition and Signatures of Lung Fibroblast Populations in Development and Fibrosis in Mice and Men 148 120 57 9 3

Defining the transcriptional landscape of infiltrating immune cells in human and mouse bladder cancer. 173 148 14 9 3

A limited set of transcriptional programs define major cell types 148 120 9

Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships 148 43 14 9

A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations 148 120 43 9 3

Single cell analysis of colorectal cancer identifies mitogen-activated protein kinase as a key driver of tumor cell plasticity 152 148 142 14 9 3

Single-cell RNA sequencing reveals functional heterogeneity and sex differences of glioma-associated brain macrophages 148 120 9 3

Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics 148 14 9 3

Single cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cells 148 120 9

Single cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse immune cell subtypes including T-bet+ B cells 148 43 27 9

Comparative analysis of human brain organoids of brainstem and midbrain at single-cell resolution 148 43 9

Flow cytometric analysis and purification of airway epithelial cell subsets 148 43 9 3

Dissecting Mammalian Spermatogenesis Using Spatial Transcriptomics 148 43 9

Transcriptome sequencing and multi-plex imaging of prostate cancer microenvironment reveals a dominant role for monocytic cells in progression 148 14 9 3

Kidney single-cell atlas reveals myeloid heterogeneity in progression and regression of kidney disease. 148 27 10 9 3

Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer 148 120 9 3

Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults 148 41 9

Resolving the spatial and cellular architecture of lung adenocarcinoma by multi-region single-cell sequencing 148 120 14 9 3

Single-cell analyses of the corneal epithelium: Unique cell types and gene expression profiles 148 120 20 9 3

Cells and gene expression programs in the adult human heart 148 120 9 3

Human Prostate Cancer-Associated Macrophage Subtypes with Prognostic Potential Revealed by Single-cell Transcriptomics 189 148 14 9 3

Single-cell Transcriptomics Identify Extensive Heterogeneity in the Cellular Composition of Mouse Achilles Tendons 148 120 9 3

Consensus transcriptional states describe human mononuclear phagocyte diversity in the lung across health and disease 148 120 9

Elucidation of tumor-stromal heterogeneity and the ligand-receptor interactome by single cell transcriptomics in real-world pancreatic cancer biopsies 152 148 14 9 4

Single-cell analysis reveals diverse stromal subsets associated with immune evasion in triple-negative breast cancer 148 14 9 3

Transcriptional network analysis of transcriptomic diversity in resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system. 148 120 27 9

Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy 152 14 9 3

Transcriptomic profiling of human effector and regulatory T cell subsets identifies predictive population signatures 88 27 9 3

Surveying Brain Tumor Heterogeneity by Single-Cell RNA Sequencing of Multi-sector Biopsies 173 148 43 9

Single nucleus RNASeq profiling of mouse lung: reduced dissociation bias and improved detection of rare cell types compared with single cell RNASeq 148 120 43 9

The cellular genomic diversity, regulatory states and networking of the metastatic colorectal cancer microenvironment 148 14 9 3

Urine single cell RNA-sequencing in focal segmental glomerulosclerosis reveals inflammatory signatures in immune cells and podocytes 148 98 9

Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment 152 148 14 9

Single cell RNA-seq reveals immunosuppressive gastric stem-like cancer cells as a poor prognostic factor 148 14 9 3

Bayesian cell-type deconvolution and gene expression inference reveals tumor-microenvironment interactions 43 9 4

Single-cell RNA-seq reveals identity and heterogeneity of malignant osteoblast cells and TME in osteosarcoma 148 14 9 3

Defining human mesenchymal and epithelial heterogeneity in response to oral inflammatory disease 148 120 27 3

Single-cell transcriptome profiling an adult human cell atlas of 15 major organs 120 9 3

A Pan-Cancer Blueprint of the Heterogeneous Tumour Microenvironment Revealed by Single-Cell Profiling 148 43 14 9

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis 43 9 4

Single-cell analysis reveals cellular heterogeneity and molecular determinants of hypothalamic leptin-receptor cells 148 120 43 9 3

Unsupervised cell interaction profiling reveals major architectural differences between small intestinal and colonic epithelial crypts 148 57 43 20 9

A novel single-cell based method for breast cancer prognosis 43 26 4

Single cell transcriptome profiling of the Atlantic cod immune system 148 88 27 9

Mouse Aging Cell Atlas Analysis Reveals Global and Cell Type Specific Aging Signatures 120 43 9

Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas 148 120 9

An integrated analysis of myeloid cells identifies gaps in in vitro models of in vivo biology 148 57 9

Global computational alignment of tumor and cell line transcriptional profiles 43 14 9 4

Single-Cell Analysis of Hyperthermic Intraperitoneal Chemotherapy Treated Tumors Reveals Distinct Cellular and Molecular Responses 148 14 9 3

Dynamic Analysis of Alternative Polyadenylation from Single-Cell RNA-Seq(scDaPars) Reveals Cell Subpopulations Invisible to Gene Expression Analysis 43 9 4 3

Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing to Define Immune Cell Chimerism in the Rejecting Kidney Transplant 148 88 9

Mapping multicellular programs from single-cell profiles 43 9

Transcriptional and Cellular Diversity of the Human Heart 120 9

Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohns disease 148 57 20 9 3

The impact of chromatin remodeling on gene expression at the single cell level in Arabidopsis thaliana 43 31 9 3

Single-cell Transcriptomics Identifies Gene Expression Networks Driving Differentiation and Tumorigenesis in the Human Fallopian Tube 148 120 9 3

A molecular map of lymph node blood vascular endothelium at single cell resolution 148 94 88 20 3

Joint single cell DNA-Seq and RNA-Seq of gastric cancer reveals subclonal signatures of genomic instability and gene expression 43 9 4

Spatially-Resolved Live Cell Tagging and Isolation Using Protected Photoactivatable Cell Dyes 148 18 9

Extensive Intratumor Proteogenomic Heterogeneity Revealed by Multiregion Sampling in High-Grade Serous Ovarian Tumor Specimens 148 14 9

A systematic dissection of human primary osteoblasts in vivo at single-cell resolution 120 43 9 3

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts 120 9 3

Transcriptional subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer 152 14 9 3

Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis. 73 27 9 1

Neoplastic and Immune single cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma. 148 120 9

Combined single-cell gene and isoform expression analysis in haematopoietic stem and progenitor cells 43 9 3

Heterogeneity of Neuroepithelial Cells and Radial Glia 133 120 20 9

Single-nucleus RNA-seq2 reveals a functional crosstalk between liver zonation and ploidy 148 43 9

Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution 43 9 4

Novel Human Kidney Cell Subsets Identified by Mux-Seq 43 9 4

A molecular cell atlas of the human lung from single cell RNA sequencing 120 9

Probabilistic gene expression signatures identify cell-types from single cell RNA-seq data 43 4

Single-cell RNA sequencing deconvolutes the in vivo heterogeneity of human bone marrow-derived mesenchymal stem cells 148 57 9 3

Molecular taxonomy of human ocular outflow tissues defined by single cell transcriptomics 148 120 9 3

Reconstruction of cell spatial organization based on ligand-receptor mediated self-assembly 43 9 4

Molecular determinants and heterogeneity of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing 88 27 9 3

Integrative transcriptomic analysis of SLE reveals IFN-driven cross-talk between immune cells 175 120 9

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier 43 26 4

Single-cell transcriptomic analysis identifies neocortical developmental differences between human and mouse 120 43 9 3

Transcriptome profiling of the branchial arches reveals cell type composition and a conserved signature of neural crest cell invasion 120 118 20 9 3

Clump sequencing exposes the spatial expression programs of intestinal secretory cells 148 43 9

Fragmentation of Small-cell Lung Cancer Regulatory States in Heterotypic Microenvironments 148 14 9 3

Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis 148 120 9

Establishment of a simplified preparation method for single-nucleus RNA-sequencing and its application to long-term frozen tumor tissues 175 43 4

Single cell transcriptional profiling reveals helper, effector, and regulatory MAIT cell populations enriched during homeostasis and activation 88 27 9 3

Whole-organism mapping of the genetics of gene expression at cellular resolution 19 9 4

Transcriptome analysis of IPF fibroblastic foci identifies key pathways involved in fibrogenesis 148 120 9 3

Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers 120 43 9

Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses 43 9 4

Airway-associated macrophages in homeostasis and repair 148 27 10 3

Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung revealed at single cell resolution 148 20 3

An atlas of cell types in the mammalian epididymis and vas deferens 120 9 3

Human and mouse transcriptome profiling identifies cross-species homology in pulmonary and lymph node mononuclear phagocytes 148 120 27 9

Circulating Clonally Expanded T Cells Reflect Functions of Tumor Infiltrating T Cells 173 88 14 9 3

SPOTlight:Seeded NMF regression to Deconvolute Spatial Transcriptomics Spots with Single-Cell Transcriptomes 43 9 4

Single-cell RNA-seq of the stromal vascular fraction of adipose tissue reveals lineage-specific changes in cancer-related lymphedema 120 9 3

Phenotype-guided subpopulation identification from single-cell sequencing data 147 43 4

Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics 116 50 11 9 2

Deterministic scRNA-seq of individual intestinal organoids reveals new subtypes and coexisting distinct stem cell pools 148 43 18 9

Evolving Transcriptomic Signature of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium Cells With Age 57 9 3