Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells

Figure 2

Explorative analysis of ATAC-seq and RNA-seq samples. (a) Principal component analysis (PCA) was carried out on CQN-normalized ATAC-seq data given as centered by mean subtraction for each feature (genomic region). PC1 and PC2 are shown, along with the % variation explained. Symbol colors indicate the given cell populations and symbol shapes and fillings represent individual donors (–6 donors) as in Figure 1(c). Data from technical replicates were pooled before analysis. (b) PCA for RNA-seq data given as centered by mean subtraction for each feature (gene). Labels as in (a). (c, d) t-SNE dimensionality reduction visualization of (c) ATAC-seq and (d) RNA-seq data, processed and labeled as in (a) and (b), respectively.

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