GZNL's Respiratory Data Centre, GZNL-RDC

Developmental Lung Cell Atlas

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DOI Author Year Title Accession code Seq technology Seq method Species Donor status Organ Region Developmental stage Cloud drive link
10.1183/13993003.00474-2022 Valenzi et al Eur Respir J 2023 Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity. GSE214085 10X scRNA-seq Homo sapiens Idiopathic pulmonary fibrosis (IPF) Lung Lung Unclassified Link
10.1016/j.cell.2021.01.053 Ren et al Cell 2021 COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas GSE158055 10X scRNA-seq Homo sapiens COVID-19 Lung Bronchi, Lung, Pharynx Adult Link
10.1038/s41467-024-48700-8 Zuani et al Nat Commun 2024 Single-cell and spatial transcriptomics analysis of non-small cell lung cancer E-MTAB-13526 10X scRNA-seq Homo sapiens NSCLC, lung squamous cell carcinoma, lung adenocarcinoma,healthy Lung Lung Adult Link
10.1038/s41588-024-01702-0 Natri et al Nat Genet 2024 Cell-type-specific and disease-associated expression quantitative trait loci in the human lung GSE227136 10X scRNA-seq Homo sapiens Idiopathic pulmonary fibrosis (IPF) Lung Lung Adult,Children Link
10.1038/s41586-021-03752-4 Caushi et al Nature 2021 Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. GSE176021 10X scRNA-seq Homo sapiens NSCLC Tumor Lung Unclassified Link
10.1164/rccm.202401-0078OC Zhao et al Am J Respir Crit Care Med 2024 Single-Cell Analysis Reveals Novel Immune Perturbations in Fibrotic Hypersensitivity Pneumonitis GSE271789 10X scRNA-seq Homo sapiens IPF, Fibrotic HP Bronchi Alveolar Adult Link
10.1038/s41587-022-01495-9 Ursu et al Nat Biotechnol 2022 Author Correction: Massively parallel phenotyping of coding variants in cancer with Perturb-seq GSE161824 10X scRNA-seq Homo sapiens Lung cancer Lung Lung Unclassified Link
10.1038/s41590-024-02064-9 Coates et al Nat Immunol 2025 Temporal profiling of human lymphoid tissues reveals coordinated defense against viral challenge GSE287808 10X scRNA-seq Homo sapiens COVID-19 Nose Nasal cavity Adult Link
10.1016/j.xcrm.2021.100476 Cillo et al Cell Rep Med 2021 People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden GSE180578 10X scRNA-seq Homo sapiens COVID-19, ARDS Lung lung Adult Link
10.1136/thorax-2022-219958 Stoleriu et al Thorax 2024 COPD basal cells are primed towards secretory to multiciliated cell imbalance driving increased resilience to environmental stressors. GSE233145 Drop-seq scRNA-seq Homo sapiens Chronic obstructive pulmoriary disease(COPD) Bronchi Bronchi Adult,Children Link
10.1242/dev.177428 García et al Development 2019 Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures GSE121600 10X scRNA-seq Homo sapiens Healthy Bronchi, Nose, Airway Bronchi, Nose, Airway Unclassified Link
10.1172/JCI183978 Zhao et al J Clin Invest 2024 Activation of STAT3-mediated ciliated cell survival protects against severe infection by respiratory syncytial virus. GSE274466 10X scRNA-seq Homo sapiens Healthy Airway Airway Adult,Newborn Link
10.1126/sciadv.aba1983 Adams et al Sci Adv 2020 Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis GSE136831 10X scRNA-seq Homo sapiens Idiopathic pulmonary fibrosis (IPF) ,Chronic obstructive pulmoriary disease(COPD) Lung Lung Adult Link
10.1016/j.xcrm.2024.101615 Zhang et al Cell Rep Med 2024 Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104) GSE241934 10X scRNA-seq Homo sapiens Lung Adenocarcinoma(LUAD) lung Lung Adult Link
10.1038/s41586-018-0394-6 Plasschaert et al Nature 2018 A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte GSE102580 InDrops scRNA-seq Homo sapiens Healthy Bronchi Lung Adult Link
10.1038/s41556-022-01064-x Sountoulidis et al Nat Cell Biol 2023 A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung GSE215895 10X scRNA-seq Homo sapiens Healthy Lung Lung lobe Fetal Link
10.1038/s41587-021-01037-9 Loske et al Nature Biotechnology 2021 Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children EGAS00001005461 10X scRNA-seq Homo sapiens SARS-CoV-2 Airway Airway Adult,Children,Newborn Link
10.1038/s41586-021-04345-x Yoshida et al Nature 2022 Local and systemic responses to SARS-CoV-2 infection in children and adults GSE168215 10X scRNA-seq Homo sapiens COVID-19 Nose, Bronchi, Trachea Nose, Bronchi, Trachea Adult,Children Link
10.15252/emmm.202012871 Mayr et al EMBO Mol Med 2021 Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers 2020_Mayr Drop-seq scRNA-seq Homo sapiens Lung Adenocarcinoma(LUAD), lung squamous cell carcinoma(LUSC) EPCAM+ Epithelium, PTPRC+ Leukocytes, COL1A2+ Mesenchyme, CLDN5+ Endothelium Lung Adult Link
10.1126/sciimmunol.adg1487 Dykema et al Sci Immunol 2023 Lung tumor-infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response GSE235500 10X scRNA-seq Homo sapiens NSCLC lung Lung Adult Link
10.1126/sciadv.aba1972 Habermann et al Science Advances 2020 Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis GSE135893 10X scRNA-seq Homo sapiens Idiopathic pulmonary fibrosis (IPF) , chronic hypersensitivity pneumonitis , nonspecific interstitial pneumonia , sarcoidosis , unclassifiable ILD , nonfibrotic controls Lung Lung Adult Link
10.1158/1541-7786.MCR-22-0881 Wollenzien et al Mol Cancer Res 2023 Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer GSE216182 10X scRNA-seq Homo sapiens SCLC Lung Lung Adult Link
10.1016/j.ccell.2023.03.009 Pai et al Cancer Cell 2023 Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade. GSE185206 10X scRNA-seq Homo sapiens Lung cancer Lung Lung Unclassified Link
10.1126/sciadv.adl4913 Hasegawa et al Sci Adv 2024 Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis GSE288887 10X scRNA-seq Homo sapiens coal-workers pneumoconiosis lung Lung Adult Link
10.1038/s41467-020-16164-1 Kim et al Nature computation 2020 Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma GSE131907 10X scRNA-seq Homo sapiens Lung Adenocarcinoma(LUAD) Lung Lung Adult Link
10.1038/s41588-022-01243-4 Madissoon et al Nature genetic 2022 A spatially resolved atlas of the human lung characterizes a gland-associated immune niche S-SUBS17 10X scRNA-seq,snRNA-seq Homo sapiens Healthy Bronchi, Lung, Trachea Bronchi, Parenchyma, Trachea Adult Link
10.1002/jmv.29889 Wang et al J Med Virol 2024 Interferon-responsive neutrophils and macrophages extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis. GSE263469 10X scRNA-seq Homo sapiens COVID-19 Lung Alveolar Adult Link
10.1038/s41586-021-03570-8 Delorey et al Nature 2021 COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets GSE171668 10X snRNA-seq Homo sapiens COVID-19 Lung Lung Adult Link
10.3390/cells13231991 Kim et al Cells 2024 Transcriptomic Analysis of Air-Liquid Interface Culture in Human Lung Organoids Reveals Regulators of Epithelial Differentiation. GSE280502 10X scRNA-seq Homo sapiens Healthy Lung Lung Adult Link
10.1126/sciimmunol.adf9988 Barnes et al Sci Immunol 2023 Early human lung immune cell development and its role in epithelial cell fate. E-MTAB-11528 Cite-seq scRNA-seq Homo sapiens Healthy Lung Lung Fetal Link
10.1038/s41586-020-03148-w Grant et al Nature 2021 Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia GSE155249 10X scRNA-seq Homo sapiens COVID-19 Lung Lung Adult Link
10.1172/jci.insight.176596 Mellors et al JCI insight 2025 Shared roles of immune and stromal cells in the pathogenesis of human bronchiolitis obliterans syndrome. GSE290834 10X scRNA-seq Homo sapiens CLAD-BOS, cGVHD-BOS Lung Distal lung Adult Link
10.1038/s41467-021-21043-4 Liu et al Nat Commun 2021 Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution GSE162025 10X scRNA-seq Homo sapiens nasopharyngeal carcinom Pharynx Nasopharynx Adult Link
10.1016/j.celrep.2024.114076 Meganck et al Cell Rep 2024 SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia GSE253698 10X scRNA-seq Homo sapiens COVID-19 Airway Airway Adult,Unclassified Link
10.1158/1078-0432.CCR-24-2983 Rosner et al Clin Cancer Res 2025 Divergent Clinical and Immunologic Outcomes Based on STK11 Co-mutation Status in Resectable KRAS-Mutant Lung Cancers Following Neoadjuvant Immune Checkpoint Blockade GSE280232 10X scRNA-seq Homo sapiens lung cancer lung Lung Adult Link
10.1038/s41586-022-04552-0 Basil et al Nature 2022 Human distal airways contain a multipotent secretory cell that can regenerate alveoli GSE168191 10X scRNA-seq Homo sapiens Chronic obstructive pulmoriary disease(COPD) Lung Periphery, Proximal airway Adult Link
10.1016/j.omtn.2021.06.010 Cooney et al Mol Ther Nucleic Acids 2024 Lentiviral vectors transduce lung stem cells without disrupting plasticity. GSE159056 10X scRNA-seq Homo sapiens Cystic Fibrosis (CF) Airway Airway Unclassified Link
10.1038/s41419-023-05992-w Wang et al Cell Death Dis 2023 Multidirectional characterization of cellular composition and spatial architecture in human multiple primary lung cancers GSE200972 10X scRNA-seq Homo sapiens Multiple primary lung cancers Lung Lung Adult Link
10.1038/s41587-020-0602-4 Chua et al Nature Biotechnology 2020 COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis EGAS00001004481 10X scRNA-seq Homo sapiens COVID-19 Airway Airway Adult Link
10.1038/s41467-021-21702-6 Bost et al Nat Commun 2021 Deciphering the state of immune silence in fatal COVID-19 patients GSE157344 10X scRNA-seq Homo sapiens COVID-19 Lung Lung Adult Link
10.1016/j.isci.2024.110009 Chang et al iScience 2024 Uncovering strain- and age-dependent innate immune responses to SARS-CoV-2 infection in air-liquid-interface cultured nasal epithelia GSE241292 10X scRNA-seq Homo sapiens COVID-19 Nose Nose Adult,Children Link
10.1126/sciimmunol.abf6692 Zhao et al Sci Immunol 2021 Clonal expansion and activation of tissue-resident memory-like Th17 cells expressing GM-CSF in the lungs of severe COVID-19 patients GSE167118 Cite-seq scRNA-seq Homo sapiens COVID-19 and Bacterial pneumonia Lung,Blood Lung: BALF , Blood Adult Link
10.1126/scitranslmed.abe4282 Bharat et al Sci Transl Med 2020 Lung transplantation for patients with severe COVID-19. GSE158127 10X scRNA-seq Homo sapiens COVID-19 Parenchyma, Bronchi Parenchyma, Bronchi Adult Link
10.1183/13993003.02725-2021 Hönzke et al Eur Respir J 2022 Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages GSE198864 10X snRNA-seq Homo sapiens COVID-19 Lung Lung Unclassified Link
10.1128/spectrum.00776-23 Cohen et al Microbiol Spectr 2023 Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single-cell RNA sequencing GSE189900 10X scRNA-seq Homo sapiens Lung adenocarcinoa Airway Airway Adult Link
10.1038/s41467-024-50281-5 Quach et al Nat Commun 2024 Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity GSE264407 10X scRNA-seq Homo sapiens Healthy Lung Lung Fetal Link
10.1038/s41467-023-42327-x Dolgalev et al Nat Commun 2023 Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma GSE229253 10X scRNA-seq Homo sapiens Lung Adenocarcinoma(LUAD) lung Lung Adult Link
10.1038/s12276-022-00896-9 Zhu et al Exp Mol Med 2022 Delineating the dynamic evolution from preneoplasia to invasive lung adenocarcinoma by integrating single-cell RNA sequencing and spatial transcriptomics. GSE189357 10X scRNA-seq Homo sapiens Lung Adenocarcinoma(LUAD) Lung Lung Adult Link
10.1126/scitranslmed.adn0136 Li et al Sci Transl Med 2024 Comparative single-cell analysis reveals IFN-γ as a driver of respiratory sequelae after acute COVID-19 GSE263817 10X scRNA-seq Homo sapiens R-PASC, Non-R-PASC Bronchi Alveolar Adult Link
10.1016/j.ajt.2024.08.019 Wong et al Am J Transplant 2024 Ischemia-reperfusion responses in human lung transplants at the single-cell resolution GSE220797 10X scRNA-seq Homo sapiens Ischemia reperfusion Lung Periphery Adult Link
10.1038/s41388-021-02054-3 Bischoff et al Oncogene 2021 Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma https://codeocean.com/capsule/8321305/tree/v2 10X scRNA-seq Homo sapiens Lung Adenocarcinoma(LUAD) Lung Lung Adult Link
10.1172/JCI148517 Ahn et al Journal of Clinical Investigation 2021 Nasal ciliated cells are primary targets for SARS-CoV-2 replication in the early stage of COVID-19 GSE164547 10X scRNA-seq Homo sapiens COVID-19 Pharynx Nasopharynx Adult Link
10.7554/eLife.62522 Wang et al Elife 2020 Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes GSE161382 10X snRNA-seq Homo sapiens Healthy Lung Lung lobe Adult,Children,Newborn Link
10.1007/s13238-020-00752-4 He et al Protein Cell 2020 Single-cell analysis reveals bronchoalveolar epithelial dysfunction in COVID-19 patients GSE147143 10X scRNA-seq Homo sapiens COVID-19 Lung Lung Adult Link
10.1038/s41586-021-03569-1 Melms et al Nature 2021 A molecular single-cell lung atlas of lethal COVID-19 GSE171524 10X snRNA-seq Homo sapiens COVID-19 Lung Lung Adult Link
10.26508/lsa.202201458 Li et al Life Sci Alliance 2022 ScRNA-seq expression of IFI27 and APOC2 identifies four alveolar macrophage superclusters in healthy BALF. GSE193782 10X scRNA-seq Homo sapiens Cystic Fibrosis (CF) lung Lung Adult Link
10.1158/2767-9764.CRC-23-0167 Yanagihara et al Cancer Res Commun 2023 A Th1-like CD4+ T-cell Cluster That Predicts Disease-free Survival in Early-stage Lung Cancer GSE215219 10X scRNA-seq Homo sapiens Lung cancer Lung Lung Adult Link
10.1126/science.abl5197 Conde et al Science 2022 Cross-tissue immune cell analysis reveals tissue-specific features in humans E-MTAB-11536 10X scRNA-seq Homo sapiens Healthy Lung Lung Adult Link
10.1126/sciimmunol.abd5778 Gueguen et al Sci Immunol 2021 Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer GSE162498 10X scRNA-seq Homo sapiens NSCLC Lung Lung Adult Link
10.1038/s41586-020-2056-8 Wu et al Nature 2020 Peripheral T cell expansion predicts tumour infiltration and clinical response GSE139555 10X scRNA-seq Homo sapiens Lung adenocarcinoma; Lung squamous cell carcinoma, nonkeratinizing; Lung squamous cell carcinoma, keratinizing; Large cell neuroendocrine carcinoma lung Lung Adult Link
10.1038/s41591-020-0901-9 Liao et al Nat Med 2020 Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19 GSE145926 10X scRNA-seq Homo sapiens COVID-19 Bronchi Lung Adult Link
10.1002/ctm2.300 Tao et al Clin Transl Med 2021 Preliminary analyses of scRNA sequencing and immunohistochemistry of children's lung tissues indicate the expression of SARS-CoV-2 entry-related genes may not be the key reason for the milder syndromes of COVID-19 in children GSE155900 10X scRNA-seq Homo sapiens Healthy lung Lung Children Link
10.1186/s13073-023-01164-9 Hu et al Genome Med 2023 Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing GSE207422 BD Rhapsody scRNA-seq Homo sapiens NSCLC lung Lung Adult Link
10.1016/j.ccell.2021.09.008 Chan et al Cancer Cell 2021 Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer https://data.humantumoratlas.org/publications/msk_sclc_chan_2021?tab=scrna-seq 10X scRNA-seq Homo sapiens SCLC lung Lung Adult Link
10.1038/s41467-021-22801-0 Wu et al Nat Communs 2021 Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer GSE148071 GEXSCOPE scRNA-seq Homo sapiens Lung cancer lung Lung Adult Link
10.1016/j.cell.2022.11.005 He et al Cell 2022 A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates E-MTAB-11278 10X scRNA-seq Homo sapiens Healthy Lung Proximal lung, Whole lung, Distal lung Fetal Link
10.1007/s00018-024-05322-z Vu Manh et al Cell Mol Life Sci 2024 SARS-CoV2 infection in whole lung primarily targets macrophages that display subset-specific responses. GSE246128 10X scRNA-seq Homo sapiens Alcoholism, High blood pressure, Alcoholism - Diabete Lung Lung lobe Adult Link
10.1016/j.jaci.2024.04.021 Ruysseveldt et al J Allergy Clin Immunol 2024 The nasal basal cell population shifts toward a diseased phenotype with impaired barrier formation capacity in allergic rhinitis. GSE261706 10X scRNA-seq Homo sapiens Allergic rhinitis Nose Nasal cavity Adult Link
10.1126/science.abl4896 Consortium et al Science 2022 The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. GSE201333 Smart-seq2 scRNA-seq Homo sapiens Chronic lung disease Lung,Blood Lung, PBMC Adult Link
10.1038/s41467-020-15647-5 Tsukui et al Nat Communs 2020 Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis GSE132771 10X scRNA-seq Homo sapiens Idiopathic pulmonary fibrosis (IPF) , Scleroderma Lung Lung Unclassified Link
10.1172/jci.insight.167082 Khatri et al JCI Insight 2023 JAK-STAT activation contributes to cytotoxic T cell-mediated basal cell death in human chronic lung allograft dysfunction. GSE224210 10X scRNA-seq Homo sapiens Chronic lung allograft dysfunction Lung Lung Adult,Children Link
10.1038/s41467-024-49756-2 Neyton et al Nat Commun 2024 Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19 GSE236030 10X scRNA-seq Homo sapiens COVID-19 Trachea Trachea Adult Link
10.1172/jci.insight.180198 Koenitzer et al JCI Insight 2024 Transcriptional analysis of primary ciliary dyskinesia airway cells reveals a dedicated cilia glutathione pathway. GSE272189 10X scRNA-seq Homo sapiens Primary ciliary dyskinesia Airway Airway Adult,Children Link
10.1164/rccm.201911-2199OC Deprez et al Am J Respir Crit Care Med 2020 A Single-Cell Atlas of the Human Healthy Airways GSE143868 10X scRNA-seq Homo sapiens Healthy Airway Airway, Nasal cavity Adult Link
10.1165/rcmb.2024-0232LE Blackburn et al Am J Respir Cell Mol Biol 2025 A Single-Cell RNA Sequencing Atlas of the Chronic Obstructive Pulmonary Disease Distal Lung to Predict Cell-Cell Communication. GSE269390 10X scRNA-seq Homo sapiens chronic obstructive pulmonary disease Lung Distal lung Adult Link
10.1172/jci.insight.177729 Bai et al JCI Insight 2024 Increased autoreactivity and maturity of EBI2+ antibody-secreting cells from nasal polyps GSE270953 10X,Cite-seq scRNA-seq Homo sapiens Chronic Rhinosinusitis with Nasal Polyps (CRSwNP) Nose Nasal cavity Adult Link
10.1038/s41467-023-43223-0 Morrell et al Nat Commun 2023 The transcriptional and phenotypic characteristics that define alveolar macrophage subsets in acute hypoxemic respiratory failure. GSE234918 Cite-seq scRNA-seq Homo sapiens ARDS, AHRF Lung Alveolar Adult Link
10.21203/rs.3.rs-2870695/v1 Choi et al Res Sq 2023 Organoid modeling of lung-resident immune responses to SARS-CoV-2 infection GSE216049 10X scRNA-seq Homo sapiens Healthy lung Lung Adult Link
10.1164/rccm.201712-2410OC Reyfman et al American journal of respiratory and critical care medicine 2019 Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis GSE122960 10X scRNA-seq Homo sapiens Systemic sclerosis_associated ILD; IPF; Hypersensitivity pneumonitis; Myositis-associated ILD Lung Lung Adult Link
10.1172/JCI174598 Cohen et al J Clin Invest 2024 A fibroblast-dependent TGF-β1/sFRP2 noncanonical Wnt signaling axis promotes epithelial metaplasia in idiopathic pulmonary fibrosis GSE239664 10X scRNA-seq Homo sapiens fibrotic lung, idiopathic pulmonary fibrosis lung Lung Adult Link
10.1016/j.jinf.2023.09.004 Wang et al J Infect 2023 Single-cell RNA-sequencing reveals heterogeneity and intercellular crosstalk in human tuberculosis lung GSE192483 10X scRNA-seq Homo sapiens tuberculosis lung Lung Adult Link
10.1172/jci.insight.139019 Sana Siddiqui et al JCI Insight 2021 Epithelial miR-141 regulates IL-13-induced airway mucus production GSE164015 10X scRNA-seq Homo sapiens Asthma Bronchi Bronchi Unclassified Link
10.1371/journal.pbio.3001143 Ravindra et al PLoS Biol 2021 Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. GSE166766 10X scRNA-seq Homo sapiens Healthy Bronchi Bronchi Unclassified Link
10.1126/sciimmunol.abk1741 Cheon et al Sci Immuno 2021 Immune signatures underlying post-acute COVID-19 lung sequelae GSE176201 10X scRNA-seq Homo sapiens COVID-19 Lung,Blood BAL, PBMC Adult Link
10.3389/fimmu.2024.1372658 Mehta et al Front Immunol 2024 Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease GSE228236 10X scRNA-seq Homo sapiens subacute inflammation, pulmonary fibrosis Bronchi Alveolar Adult Link
10.1038/s41467-021-21795-z Gong et al Nat Communs 2021 Comprehensive single-cell sequencing reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of nasopharyngeal carcinoma GSE150825 10X scRNA-seq Homo sapiens nasopharyngeal carcinom Pharynx Nasopharynx Adult Link
10.1084/jem.20220126 Liu et al J Exp Med 2022 HER2 drives lung fibrosis by activating a metastatic cancer signature in invasive lung fibroblasts GSE137026 10X scRNA-seq Homo sapiens idiopathic pulmonary fibrosis, Invasive lung fibroblasts, Non-invasive lung fibroblasts Lung Lung Adult,Children Link
10.1183/13993003.02441-2018 Morse et al Eur Respir J 2019 Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis GSE128033 10X scRNA-seq Homo sapiens Idiopathic pulmonary fibrosis (IPF) Lung, Bronchi Lung lobe, Lung Adult Link
10.1016/j.immuni.2023.01.032 Wang et al Immunity 2023 Dysregulated lung stroma drives emphysema exacerbation by potentiating resident lymphocytes to suppress an epithelial stem cell reservoir GSE196638 10X scRNA-seq Homo sapiens Chronic obstructive pulmoriary disease(COPD) Lung Distal lung Adult Link
10.1016/j.isci.2021.102151 Wyler et al iScience 2021 Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy. GSE148729 Drop-seq scRNA-seq Homo sapiens SARS-CoV-2 Lung Lung Unclassified Link
10.1038/s41590-024-01885-y Jaeger et al Nat Immunol 2024 Diversity of group 1 innate lymphoid cells in human tissues GSE240441 10X scRNA-seq Homo sapiens pulmonary fibrosis Lung, Pharynx Lung, Pharynx Adult,Children Link
10.1038/s42003-025-08066-z Detsika et al Commun Biol 2025 CD55 upregulation in T cells of COVID-19 patients suppresses type-I interferon responses. GSE293707 10X scRNA-seq Homo sapiens COVID-19 Lung Lung Adult Link
10.1016/j.xgen.2022.100229 Koh et al Cell Genom 2024 Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma. GSE185199 10X scRNA-seq Homo sapiens Healthy Bronchi Bronchi Adult,Children Link
10.3389/fimmu.2023.1142228 Gouin et al Front Immunol 2023 Cell type- and time-dependent biological responses in ex vivo perfused lung grafts GSE218788 10X scRNA-seq Homo sapiens High blood pressure Lung Lung lobe Adult Link
10.1038/s42003-021-01897-6 Maroni et al Commun Biol 2021 Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer GSE136246 InDrops scRNA-seq Homo sapiens NSCLC Lung Lung Adult Link
10.1016/j.cell.2020.10.030 Daniloski et al Cell 2021 Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells. GSE159519 ECCITE-seq scRNA-seq Homo sapiens Lung cancer Lung Lung Unclassified Link
10.1136/annrheumdis-2018-214865 Valenzi et al Ann Rheum Dis 2020 Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease GSE128169 10X scRNA-seq Homo sapiens scleroderma Lung Lung lobe, Lung Adult Link
10.1016/j.celrep.2023.113454 Li et al Cell Rep 2023 Abundant binary promoter switches in lineage-determining transcription factors indicate a digital component of cell fate determination GSE242100 10X scRNA-seq Homo sapiens Healthy Pharynx Pharynx Unclassified Link
10.1186/s12931-022-02293-2 Huang et al Respir Res 2022 Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD. GSE171541 BD Rhapsody scRNA-seq Homo sapiens Chronic obstructive pulmoriary disease(COPD) Lung Lung Adult Link
10.3389/fonc.2023.1204726 Miller et al Front Oncol 2023 Phase Ib trial of inhaled iloprost for the prevention of lung cancer with predictive and response biomarker assessment GSE240001 10X scRNA-seq Homo sapiens Healthy Bronchi Bronchi Adult Link
10.1038/s41586-020-2922-4 Kyle et al Nature 2020 A molecular cell atlas of the human lung from single-cell RNA sequencing syn21041850 10X scRNA-seq Homo sapiens Lung cancer Lung Periphery, Bronchi Adult Link
10.1126/sciadv.adr9995 Berdnikovs et al Sci Adv 2025 Single-cell profiling demonstrates the combined effect of wheeze phenotype and infant viral infection on airway epithelial development GSE286262 10X scRNA-seq Homo sapiens wheeze, RSV-infected Nose Nose Children Link
10.1016/j.jaci.2021.11.017 Nakayama T et al Jaci 2021 Inflammatory molecular endotypes of nasal polyps derived from White and Japanese populations GSE179269 10X scRNA-seq Homo sapiens Nasal polyps Nose Nasal cavity Adult Link
10.1164/rccm.202302-0264LE Yao et al Am J Respir Crit Care Med 2023 Maladaptive TGF-β Signals to the Alveolar Epithelium Drive Fibrosis after COVID-19 Infection GSE224955 10X scRNA-seq Homo sapiens post-acute sequelae SARS-CoV-2 infection lung Lung Unclassified Link
10.1172/JCI155506 Oliva et al J Clin Invest 2022 Aging-related olfactory loss is associated with olfactory stem cell transcriptional alterations in humans. GSE184117 10X scRNA-seq Homo sapiens Healthy Nose Nose Adult Link
10.1038/s41586-020-2157-4 Han et al Nature 2020 Construction of a human cell landscape at single-cell level GSE134355 Microwell-seq scRNA-seq Homo sapiens Healthy Lung Lung Adult Link
10.1093/cei/uxae118 Osborn et al Clin Exp Immunol 2025 Single-cell analysis of lung epithelial cells reveals age and cell population-specific responses to SARS-CoV-2 infection in ciliated cells GSE254266 10X scRNA-seq Homo sapiens COVID-19 lung Lung Adult,Children Link
10.7150/jca.103656 Zhang et al J Cancer 2025 Single-Cell Sequencing Reveals PD-L1-Mediated Immune Escape Signaling in Lung Adenocarcinoma. GSE267108 10X scRNA-seq Homo sapiens Lung adenocarcinoa lung Lung lobe Adult Link
10.1186/s13059-019-1906-x Madissoon et al Genome Biology 2019 scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation PRJEB31843 10X scRNA-seq Homo sapiens Healthy Lung Parenchyma Adult Link
10.1002/cac2.12449 Kwok et al Cancer Commun (Lond) 2023 Single-cell transcriptomic analysis uncovers intratumoral heterogeneity and drug-tolerant persister in ALK-rearranged lung adenocarcinoma GSE223779 10X scRNA-seq Homo sapiens NSCLC Lung Lung Adult Link
10.1158/0008-5472.CAN-22-0112 Kagamu et al Cancer Res 2022 Single-Cell Analysis Reveals a CD4+ T-cell Cluster That Correlates with PD-1 Blockade Efficacy GSE168844 10X scRNA-seq Homo sapiens NSCLC lung Lung Unclassified Link
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