Anndata objects and codes for McCauley_Kukreja_2024

This entry contains data used in the codes uploaded on https://github.com/AllonKleinLab/paper-data/tree/master/McCauley_Kukreja_2024 for McCauley/Kukreja et. al. 2024 manuscript.

Two of the data files are generated for this manuscript. Their GEO IDs are GSE246368 (all_indrops_data.h5ad) and GSE246441 (all_10x_data.h5ad). You can find raw files submitted to GEO. 

This entry also contains 4 published disease datasets (not generated by us) put together in anndata format and processed for data analyses done in McCauley/Kukreja et. al. The GEO IDs for these datasets are: GSE135893(adata_ipf1_epithelial_processed.h5ad), GSE136831 (adata_ipf2_epithelial_processed.h5ad, adata_copd_epithelial_processed.h5ad) and GSE171524 (adata_covid_epithelial_processed.h5ad). The publications that generated these datasets are:

Habermann, A.C., Gutierrez, A.J., Bui, L.T., Yahn, S.L., Winters, N.I., Calvi, C.L., Peter, L., Chung, M.-I.I., Taylor, C.J., Jetter, C., et al. (2020). Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis. Sci Adv 6, eaba1972. 10.1126/sciadv.aba1972.

Adams, T.S., Schupp, J.C., Poli, S., Ayaub, E.A., Neumark, N., Ahangari, F., Chu, S.G., Raby, B.A., DeIuliis, G., Januszyk, M., et al. (2020). Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations  in idiopathic pulmonary fibrosis. Sci Adv 6, eaba1983. 10.1126/sciadv.aba1983.

Sauler, M., McDonough, J.E., Adams, T.S., Kothapalli, N., Barnthaler, T., Werder, R.B., Schupp, J.C., Nouws, J., Robertson, M.J., Coarfa, C., et al. (2022). Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nat Commun 13, 494. 10.1038/s41467-022-28062-9.

Melms, J.C., Biermann, J., Huang, H., Wang, Y., Nair, A., Tagore, S., Katsyv, I., Rendeiro, A.F., Amin, A.D., Schapiro, D., et al. (2021). A molecular single-cell lung atlas of lethal COVID-19. Nature 595, 114–119. 10.1038/s41586-021-03569-1.