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Single-Cell RNA-seq (52) · 9 data types available

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Studies are listed by modality, then by sample count, highest first. Other modalities names each assay another study ran on these same samples; one such study links to it, several link to this study's Sample Network.

Modality	Species	Citation	Study	Samples	Other modalities

Dataset	Species	Stage	Cell Count
Human CellCards Multi-Study CellRef 1.0 Atlas	Human	65+ years \| Adolescent \| Adult \| Child	505256
Single-cell RNA-seq analysis of Interstitial Lung Disease (ILD) subtypesupdated	Human	65+ years \| Adult	475047
Human pediatric developmental epochsupdated	Human	Adolescent \| Adult \| Child \| Infant \| Neonate	313150
Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis	Human	65+ years \| Adult	312928
CITE-Seq of COVID-19 Human Lungsupdated	Human	65+ years \| Adolescent \| Adult \| Child	302922
Single-cell RNA-seq analysis of Bronchpulmonary Dysplasia (BPD)updated	Human	Child \| Infant	250529
Respiratory Airway Secretory Cells in COPDupdated	Human	65+ years \| Adult	154872
Human lung allografts experience persistent fibrogenic shift following acute cellular rejectionnew	Human	Adolescent \| Adult	134167
Post-viral flu lung regenerationupdated	Mouse	P4-P36	123154
Single-cell RNA-seq of 13 normal, LPS-exposed, or anti-inflammatory treated third trimester Rhesus macaque lungs	Rhesus	Saccular	120042
A molecular single-cell lung atlas of lethal COVID-19	Human	65+ years \| Adult	116314
Mouse CellCards Multi-Study CellRef 1.0 Atlas	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	95658
Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis II	Human	65+ years \| Adult	76070
The genomic, epigenomic, and biophysical cues controlling the emergence of the lung alveolus	Mouse	E12.5 \| E15.5 \| E17.5-E19.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	67794
Systematic identification of 58 lung cell populations in bronchi and parenchyma from 3 normal lungs	Human	65+ years \| Adult	65662
Lower airway mucosa of allergen-induced asthma exacerbationupdated	Human	Adult	52152
Single cell transcriptomic signatures of normal human newborn, child and adult lungs	Human	Adult \| Child \| Neonate	46500
Bronchopulmonary Dysplasia with Pulmonary Hypertensionupdated	Human	Infant \| Neonate	43607
Drop-seq single-cell RNA-Seq on unsorted lung cells from E16.5 mice.	Mouse	E16.5-E17.5	35247
Drop-seq single-cell RNA-Seq on unsorted lung cells from E18.5 mice.	Mouse	E17.5-E19.5	33441
Stromal heterogeneity in the adult lung delineated by single-cell genomicsnew	Human	Adult	18966
Human iPSC-derived epithelial-mesenchymal co-culture model of pulmonary fibrosisnew	Human		18428
Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACDMPV)updated	Human	Child \| Infant \| Neonate	17836
Bronchiolitis Obliterans Syndrome Airway scRNA-Sequpdated	Human	Child	15801
Human iPSC-derived lung mesenchyme and primary developing human lung mesenchymenew	Human		14494
Drop-seq single-cell RNA-Seq on unsorted lung cells from P10 mice.	Mouse	P4-P10 \| P4-P36	13910
Drop-seq single-cell RNA-Seq on unsorted lung cells from P7 mice.	Mouse	P4-P10 \| P4-P36	12501
Single-cell multiome analysis of lymphangioleiomyomatosis (LAM)	Human	65+ years \| Adult	12361
Human pulmonary alveolar microlithiasis (PAM) scRNA-Seq with SLC34A2 (Npt2b) mutationsupdated	Human	Adult \| Child	12084
Drop-seq single-cell RNA-Seq on unsorted lung cells from P3 mice.	Mouse	P0-P3	10483
Drop-seq single-cell RNA-Seq on unsorted lung cells from P14 mice.	Mouse	P11-P20 \| P4-P36	8618
Culture impact on the transcriptomic programs of primary and iPSC-derived human alveolar type 2 cellsupdated	Human	Adult	8128
Single-cell RNA-Seq on unsorted lung cells from P1 mice.	Mouse	P0-P3	7578
Patient-specific iPSCs carrying an SFTPC mutation reveal the intrinsic alveolar epithelial dysfunction at the inception of interstitial lung disease (ILD)updated	Human	Adolescent	7337
Drop-seq single-cell RNA-Seq on unsorted lung cells from P28 mice.	Mouse	P21-P41 \| P4-P36	7321
10x single-cell RNA-Seq on unsorted lung cells from 24 year old donor	Human	Adult	6871
Single cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cells	Human	Neonate	5499
Single-cell RNA-Seq on unsorted lung cells from 1 day old human donor	Human	Neonate	2343
Single-cell RNA-Seq on unsorted lung cells from 1 day old human donor	Human	Neonate	2000
Single-cell RNA-Seq on unsorted lung cells from 21 month old human donor	Human	Child	2000
Single-cell RNA-Seq on unsorted lung cells from 9 year old human donor	Human	Child	2000
Single-cell RNA-Seq on unsorted lung cells from WT E16.5, E18.5, P1, P3, P7, P10, P14, and P28 C57BL6 mice	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	996
Single-cell RNA-Seq on unsorted lung cells from WT E16.5 C57BL6 mice	Mouse	E16.5-E17.5	218
Single-cell RNA-Seq on unsorted lung cells from WT E18.5 C57BL6 mice	Mouse	E17.5-E19.5	143
Single-cell RNA-Seq on unsorted lung cells from WT P01 C57BL6 mice	Mouse	P0-P3	130
Single-cell RNA-Seq on unsorted lung cells from WT P07 C57BL6 mice	Mouse	P4-P10 \| P4-P36	118
Single-cell RNA-Seq on unsorted lung cells from WT P28 C57BL6 mice	Mouse	P21-P41 \| P4-P36	116
Single-cell RNA-Seq on unsorted lung cells from WT P14 C57BL6 mice	Mouse	P11-P20 \| P4-P36	115
Single-cell RNA-Seq on unsorted lung cells from WT P03 C57BL6 mice	Mouse	P0-P3	107
Single-cell RNA-Seq on unsorted lung cells from WT P10 C57BL6 mice	Mouse	P4-P10 \| P4-P36	75
Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseasesnew	Human	65+ years \| Adult	133327
Aberrant cellular communities underlying disease heterogeneity in chronic obstructive pulmonary diseasenew	Human	65+ years \| Adult	123076

Dataset	Species	Stage	Tissue/Cell Type	Sample Prep	Sample Count
Bulk RNA sequencing of human pediatric lung cell populations reveals unique transcriptomic signature associated with postnatal pulmonary development	Human	Adult \| Child \| Infant \| Neonate	Mesenchymal cell \| Endothelial cell \| Epithelial cell \| Immune cell \| Mixed control cells \| Biopsy cells	Sorted cells	151
Time course RNA-seq expression profiling of alveolar parenchyma isolated using laser capture microdissection from wild-type C57BL6 mice.	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	Pre-alveolar parenchyma \| Alveolar parenchyma	LCM	29
Time course RNA-seq profiling in sorted endothelial, epithelial, immune, and mesenchymal-derived cells from WT C57BL6 mice	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Endothelial cell \| Epithelial cell \| Immune cell \| Mesenchymal derived cell	Sorted cells	26
RNA-seq expression profiling of alveolar parenchyma isolated using laser capture microdissection from human donors	Human	Child \| Infant \| Neonate	Alveolar parenchyma	LCM	19
RNA-seq profiling in sorted pulmonary mesenchyme, endothelial cells, epithelial cells, and leukocytes from three 20 month old human donors	Human	Child	Endothelial cell \| Epithelial cell \| Pulmonary mesenchyme \| Immune cell \| Mixed control cells	Sorted cells	14
Time course RNA-seq profiling in whole lung from WT C57BL6 mice	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Lung	Whole lung	10
Time course RNA-seq profiling of mouse sorted Pdgfra+ fibroblasts	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Mesenchymal derived cell	Sorted cells	4
RNA-seq profiling in sorted pulmonary mesenchyme, endothelial cells, and leukocytes from a 1 day old human donor	Human	Neonate	Immune cell \| Endothelial cell \| Pulmonary mesenchyme	Sorted cells	3
Time course RNA-seq profiling of mouse sorted AT2 cells	Mouse	P21-P41 \| P4-P10 \| P4-P36	Type II pneumocyte	Sorted cells	2

Dataset	Species	Stage	Tissue/Cell Type	Sample Prep	Sample Count	Explore
Time course NanoString mRNA expression profiling in alveolar parenchyma from WT C57BL6 mice	Mouse	E16.5-E17.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	Pre-alveolar parenchyma \| Alveolar parenchyma	LCM	43

Dataset	Species	Stage	Tissue/Cell Type	Sample Prep	Sample Count
Time course NanoString microRNA expression profiling in alveolar parenchyma from WT C57BL6 mice	Mouse	E16.5-E17.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	Pre-alveolar parenchyma \| Alveolar parenchyma	LCM	43
Time course NanoString microRNA expression profiling in alveolar parenchyma from human donors	Human	Child \| Infant \| Neonate	Alveolar parenchyma	LCM
Time course NanoString microRNA expression profiling in sorted endothelial cells and type II pneumocytes from WT C57BL6 mice	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	Endothelial cell \| Type II pneumocyte	Sorted cells

Dataset	Species	Stage	Tissue/Cell Type	Sample Prep	Sample Count
Time course proteomic profiling in alveolar parenchyma from WT C57BL6 mice.	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	Pre-alveolar parenchyma \| Alveolar parenchyma	LCM	45
Proteomics of human postnatal lung epithelial, endothelial, mesenchymal, and immune cells	Human	Child \| Infant \| Neonate	Epithelial cell \| Endothelial cell \| Mesenchymal cell \| Immune cell	Sorted cells	44
Proteomic profiling of laser capture microdissection samples of whole lung from human subjects	Human	Child \| Infant \| Neonate	Left lung upper lobe	LCM	38
Time course proteomic profiling in sorted endothelial cells and type II pneumocytes from WT C57BL6 mice	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Endothelial cell \| Type II pneumocyte	Sorted cells	32
Proteomic profiling of laser capture microdissection samples of whole lung from human subjects	Human	Adult \| Child \| Infant \| Neonate	Left lung upper lobe	LCM	19
Time course proteomic profiling in whole lung from WT C57BL6 mice	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Lung	Whole lung	16
Time course proteomic profiling in alveolar parenchyma from WT C57BL6 mice.	Mouse	E16.5-E17.5 \| P21-P41 \| P4-P10 \| P4-P36	Pre-alveolar parenchyma \| Alveolar parenchyma	LCM	15
Proteomic profiling of laser capture microdissection samples of whole lung from human subjects	Human	Child \| Infant \| Neonate	Left lung upper lobe	LCM	12
Proteomic Analysis of Human Lung Development	Human	Child \| Infant \| Neonate	Biopsy cells from right middle lobe parenchyma	Biopsy	11

Dataset	Species	Stage	Tissue/Cell Type	Sample Prep	Sample Count	Explore
Time course metabolomic profiling in whole lung from WT C57BL6 mice	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Lung	Whole lung	16

Dataset	Species	Stage	Tissue/Cell Type	Sample Prep	Sample Count
Time course lipidomic profiling in whole lung from WT C57BL6 mice	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Lung	Whole lung	16
Lipidomic profiling in sorted acinar epithelial cells, endothelial cells, mesenchymal cells, and myeloid cells from twenty month old human donors	Human	Child	Epithelial cell \| Endothelial cell \| Mesenchymal cell \| Immune cell	Sorted cells	15
Time course lipidomic profiling in sorted endothelial cells and type II pneumocytes from WT C57BL6 mice	Mouse	E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Endothelial cell \| Type II pneumocyte	Sorted cells	6
Lipidomic profiling of human sorted mixed immune cells (MIC), mixed epithelial cells (EPI), mixed endothelial cells (END) and mixed mesenchymal cells (MES) from combined right upper and right middle lobes or, in the case of the adult lung, the right middle lobe	Human	Adult \| Child \| Infant \| Neonate	Mesenchymal cell \| Endothelial cell \| Epithelial cell \| Immune cell \| Mixed control cells \| Biopsy cells	Sorted cells

Dataset	Species	Stage	Tissue/Cell Type	Sample Prep	Sample Count
Time course MeDIP-seq analysis in alveolar parenchyma isolated using laser capture microdissection from wild-type C57BL6 mice.	Mouse	P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36		LCM
Time course MeDIP-seq analysis in sorted cells from wild-type C57BL6 mice.	Mouse	E16.5-E17.5 \| E17.5-E19.5 \| P21-P41 \| P4-P10 \| P4-P36	Epithelial cell \| Endothelial cell	Sorted cells
Time course MeDIP-seq analysis in sorted cells from wild-type C57BL6 mice.	Mouse	E17.5-E19.5 \| P0-P3 \| P11-P20 \| P21-P41 \| P4-P10 \| P4-P36	Mesenchymal derived cell \| Epithelial cell \| Endothelial cell	Sorted cells
Single-nucleus ATAC-seq analysis of lymphangioleiomyomatosis (LAM)	Human	65+ years \| Adult		Single nucleus	10050
Infinium MethylationEPIC BeadChip array profiling of laser capture microdissection samples of whole lung from human subjects	Human	Adult \| Child \| Infant \| Neonate		LCM	24
Infinium MethylationEPIC BeadChip array profiling of sorted cells from human subjects	Human	Child \| Infant \| Neonate	Epithelial cell \| Endothelial cell \| Mesenchymal cell	Sorted cells

Dataset	Species	Stage	Sample Count
A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severitynew	Human		26
Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis	Human	65+ years \| Adult	23
Xenium spatial transcriptomics of Bronchopulmonary Dysplasia and matched neonatal controlsnew	Human		10
Lipidomics Imaging of Human Postnatal Lung in Health and Bronchopulmonary Dysplasianew	Human	Infant	8
U‑FLIP Multimodal Metabolic Imaging of Human Postnatal Lung in Health and Bronchopulmonary Dysplasianew	Human	Infant	8

Stain	Species	Datasets

Antibodies	Species	Datasets

Probes	Species	Datasets