Supplemental data for: Standardized pipeline for establishing, expanding, and differentiating airway and alveolar organoids from human BAL fluid
Data files
Mar 04, 2026 version files 111.41 MB
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Gellner_2025-Supplemental_Tables_and_Figures-revision.pdf
2.19 MB
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README.md
1.19 KB
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Supplemental_Video_S1.mp4
109.22 MB
Abstract
Lung organoids are versatile experimental models, but their broader use in studying human disease is limited by the scarcity of starting material and the complexity of current methods. To align organoid technology with common clinical practice, we developed airway and alveolar organoids using cells obtained from patients' bronchoalveolar lavage (BAL) fluid. Building on existing techniques, we showed that BAL is a reliable, accessible source of primary human epithelial cells, yielding airway and alveolar organoids within 10 days. Organoids can then be expanded over many passages for downstream analysis. Our streamlined methods do not require cell sorting or other complex procedures, all cells are derived from a single patient, and media are based on serum-free, chemically-defined formulations. Here, we present detailed protocols for organoid establishment, standardized passaging and phenotyping, and differentiation of both airway and alveolar models. We provide a time course of BAL-derived airway organoid differentiation at air-liquid interface, and we demonstrate proof of principle for differentiation of BAL-derived alveolar organoids in 3D culture. These methods can be readily adapted to generate and characterize organoids from lung tissue, tracheobronchial specimens, or other primary cells from humans or mice, expanding the potential to use lung organoids for disease modeling.
Dataset DOI: 10.5061/dryad.6m905qgf3
Description of the data and file structure
SUPPLEMENTAL MATERIAL
Standardized pipeline for establishing, expanding, and differentiating airway and alveolar organoids from human BAL fluid
Taryn B. Gellner, Belinda Chen, Shreyas R. Raini, Mackenzie S. Jackson, Amy K. Kraak, Sophie C. Petta, Margherita Paschini, Lynn M. Schnapp, Carla F. Kim, Monica Yun Liu
Files and variables
File: Gellner_2025-Supplemental_Tables_and_Figures-revision.pdf
Description: Supplemental Table S1 and Figures S1-S4. See individual table/figure legends.
File: Supplemental_Video_S1.mp4
Description: Supplemental Video S1. Organoid passaging techniques (steps B2 and B5 of the main text).
Human subjects data
All human specimens were obtained with written informed consent, including consent to publish de-identified data in the public domain. Data have been deidentified by removing all coded identifiers and dates (other than age in years).
