Extended Data Fig. 6: Unbiased clustering of lower airway biopsy samples of healthy volunteers and volunteers with asthma and the strategy used to divide the dataset depicted in Fig. 3.
From: A cellular census of human lungs identifies novel cell states in health and in asthma
a, t-SNE plot depicting unbiased cluster assignment of combined dataset of healthy control and asthma lower airway biopsies, highlighting EPCAM-high cell clusters (epithelial cells) in blue and other cell types in green. b, t-SNE as in a, highlighting expression of cell lineage markers. c, t-SNE plot of only epithelial cells, as defined in a. d, t-SNE as in c, showing expression of individual genes used for cell-type assignment of different epithelial subsets. e, Table depicting cell-type assignment of clusters identified in c. f, Fluorescence in situ hybridization image of lung airway biopsy of one asthma patient. Green marks FOXJ1 (ciliated marker), red marks MUC5AC (secretory marker), and blue marks DAPI (nuclei). White arrow points to areas in which both MUC5AC and FOXJ1 are co-expressed in the exact same region (yellow color) or are contained in the vicinities of one nucleus, suggesting co-expression of the transcripts in the same cell. n = 6 healthy volunteers and 6 volunteers with asthma. Full sample distribution in Fig. 3b. Panels a–e, n = 12 individuals. Panel f depicts the analysis performed in n = 1 asthma donor.
