Human pediatric developmental epochs

Maria C. Basil1
1Perelman School of Medicine, University of Pennsylvania, *Corresponding author
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Description Single-cell RNA-Seq from the lungs (proximal and distal) of human newborns, infants, adolescent, and adult (up to 42 years), using the 10x 3' version 2 or version 3 platform. At birth, the lungs undergo an abrupt physiologic change, as the function of gas exchange transitions from the placenta to the lung. Subsequent postnatal development of the lungs is marked by a rapid and profound increase in the growth of the distal airways and alveolar gas exchange compartment. Insults during this period increase the risk of developing lung disease later in life, though how early-life events affect adult disease onset remains unclear. We generated a single-cell atlas of postnatal human lung development from birth through adulthood and mapped temporally regulated gene expression changes in each cell lineage. Using this atlas, we identified disease risk-associated genes with developmentally regulated expression. These analyses reveal cell type-specific and temporally restricted expression of genes associated with adult lung disease risk, including COPD. Heritability enrichment analysis demonstrated that COPD genetic risk is enriched in genes active during early postnatal endothelial development, linking early-life vascular maturation to adult disease susceptibility. These findings characterize the early window of susceptibility for adult chronic lung diseases and establish a framework to guide mechanistic studies of disease-associated genes.
Dataset ID LMEX0000004415
Assay Type Single-cell RNA-seq
Organism Human
Stages Neonate | Infant | Child | Adolescent | Adult
Cell Count 313150
Technology 10x Genomics Chromium Single Cell Gene Expression
Reference Planer et al. (2025)
FileDescriptionSize
PedDev_CellRef2.h5adAnalysis object for the pediatric developmental epoch viewers, HDF5 AnnData, gzip compressed. 60,911 cells x 36,601 genes over the authors' 70 `subtype` states in 7 lineages, 30 donors and 46 libraries. X holds log2 counts per ten thousand and layers['counts'] the raw integer counts it was rebuilt from; obs carries the subtype, its celltype and lineage parents, the donor, the library and the developmental epoch; obsm carries the UMAP. The cells are capped at 50 per donor and subtype, drawn with a fixed seed, because the full 313,150-cell object was too slow to load in the browser.603.9 MB
PedDev_library_metadata.tsvLibrary metadata for the 46 libraries, one row each, with the donor, sex, age, developmental epoch, disease status, tissue, cell enrichment and the cells each contributes. The rows account for all 60,911 cells in the analysis object.3.6 KB
LungMAP IDAlt IDSpeciesSexAgeAge Group
LMSP0000001556EX0000003Homo sapiensMale1 monthInfant
LMSP0000001557EX0000004Homo sapiensFemale8 monthsInfant
LMSP0000001558EX0000005Homo sapiensFemale4 monthsInfant
LMSP0000001559EX0000006Homo sapiensFemale1 monthInfant
LMSP0000001560EX0000007Homo sapiensFemale17 daysNeonate
LMSP0000001561EX0000008Homo sapiensMale0 dayNeonate
LMSP0000001562EX0000014Homo sapiensMale0 dayNeonate
LMSP0000001563EX0000015Homo sapiensMale23 daysNeonate
LMSP0000001564EX0000016Homo sapiensMale26 daysNeonate
LMSP0000001565EX0000017Homo sapiensFemale1 monthNeonate
LMSP0000001566EX0000018Homo sapiensMale1 monthNeonate
LMSP0000001567EX0000019Homo sapiensFemale2 monthsInfant
LMSP0000001568EX0000020Homo sapiensFemale10 monthsInfant
LMSP0000001569EX0000021Homo sapiensMale0 dayNeonate
LMSP0000001570EX0000022Homo sapiensMale2 monthsInfant
LMSP0000001571EX0000023Homo sapiensFemale2 monthsInfant
LMSP0000001572EX0000024Homo sapiensFemale2 monthsInfant
LMSP0000001573EX0000025Homo sapiensMale1 dayNeonate
LMSP0000001574EX0000026Homo sapiensMale2 yearsChild
LMSP0000001575EX0000027Homo sapiensMale2 yearsChild
LMSP0000001576EX0000028Homo sapiensMale5 monthsInfant
LMSP0000001577GL0000004Homo sapiensFemale35 yearsAdult
LMSP0000001578GL0000104Homo sapiensMale7 daysNeonate
LMSP0000001579GL0000110Homo sapiensFemale29 yearsAdult
LMSP0000001580GL0000115Homo sapiensMale25 yearsAdult
LMSP0000001581GL0000123Homo sapiensMale17 yearsAdolescent
LMSP0000001582GL0000128Homo sapiensMale13 yearsAdolescent
LMSP0000001583GL0000187Homo sapiensFemale12 yearsAdolescent
LMSP0000001584GL0000189Homo sapiensMale42 yearsAdult
LMSP0000001585GL0000267Homo sapiensMale39 yearsAdult