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. Author manuscript; available in PMC: 2024 Jun 21.
Published in final edited form as: Nat Genet. 2023 Jul 27;55(8):1288–1300. doi: 10.1038/s41588-023-01445-4

Extended Data Fig. 4 |. Clustering and CCA-based scRNA to scATAC-seq integration robustness to subsampling. Related to Figure 2.

Extended Data Fig. 4 |

(A through C) Repeated dimensionality reduction and clustering of the scRNA and scATAC-seq datasets with three samples (AA4, C_SD3, and C_PB3) removed from the full dataset.

(A) UMAP representations of the full subsampled dataset and sub-clustered major cell groups using scRNA data. Cell compartments are labeled on the left, and cells are colored according to their high-resolution cluster labels as shown in the x-axis in (C).

(B) UMAP representations of the full dataset and sub-clustered major cell groups using scATAC data. Cell compartments are labeled on the left, and cells are colored according to their high-resolution cluster labels as shown in the y-axis in (C).

(C) Correspondence between scRNA and scATAC-seq cluster labels for the low- and high-resolution clusters in each of the subsampled datasets.

(D through F) Repeated dimensionality reduction and clustering of the scRNA and scATAC-seq datasets with 25% of the cells randomly removed from the full dataset.

(D) Same as in (A), but for the cell-subsampled dataset.

(E) Same as in (B), but for the cell-subsampled dataset.

(F) Same as in (C), but for the cell-subsampled dataset.