biostudies-literatureUnknownZhang PNICHD NIH HHSNHLBI NIH HHSThe mature mammalian lung contains ~50 different cell types that are located in precise positions along and around the airway epithelial tree. Here, we investigated how these spatial patterns are progressively established during development. Specifically, we optimized a microfluidics-enabled, deterministic barcoding-based sequencing (DBiT-seq) workflow to achieve highly sensitive spatial mapping of tissue sections from early embryonic mouse lungs. Spatial mapping of epithelial populations revealed that <i>Sox9</i> ⁺ epithelial progenitors are located throughout the epithelial tree at early stages before becoming confined to the distal ends. Spatial mapping of mesenchymal populations revealed a previously unrecognized mesenchymal cluster that expresses high levels of extracellular matrix proteins and appears to promote embryonic lung innervation. These findings provide new insights into the spatial organization and cellular dynamics underlying early lung development, and demonstrate the power of spatial transcriptomics to uncover hidden patterns and populations of cells.bioRxiv : the preprint server for biology2025.11.22.688293https://www.ebi.ac.uk/biostudies/studies/S-EPMC12697356biostudies-literatureMapping embryonic mouse lung development using enhanced spatial transcriptomics.PMC12697356R01 HD099030DP1 HD111539R01 HL164861DP2 HD111537Nelson CMGoodwin KLaw BKChan MMZhang PfalseMapping embryonic mouse lung development using enhanced spatial transcriptomics.The mature mammalian lung contains ~50 different cell types that are located in precise positions along and around the airway epithelial tree. Here, we investigated how these spatial patterns are progressively established during development. Specifically, we optimized a microfluidics-enabled, deterministic barcoding-based sequencing (DBiT-seq) workflow to achieve highly sensitive spatial mapping of tissue sections from early embryonic mouse lungs. Spatial mapping of epithelial populations revealed that <i>Sox9</i> ⁺ epithelial progenitors are located throughout the epithelial tree at early stages before becoming confined to the distal ends. Spatial mapping of mesenchymal populations revealed a previously unrecognized mesenchymal cluster that expresses high levels of extracellular matrix proteins and appears to promote embryonic lung innervation. These findings provide new insights into the spatial organization and cellular dynamics underlying early lung development, and demonstrate the power of spatial transcriptomics to uncover hidden patterns and populations of cells.2025-01-01T00:00:00Z2025 Nov2026-06-04T03:21:28.732Z2026-06-04T03:12:45.094ZS-EPMC126973564139465510.1101/2025.11.22.688293