Extended Data Fig. 4: Quality control of chromatin accessibility data and gene ontology analysis. | Nature Neuroscience

Extended Data Fig. 4: Quality control of chromatin accessibility data and gene ontology analysis.

From: Response of spatially defined microglia states with distinct chromatin accessibility in a mouse model of Alzheimer’s disease

Extended Data Fig. 4

(a) Heat map displaying chromatin accessibility in consensus ATAC-Seq peak set (59,293 total peaks) across all samples. Each column of the heat map corresponds to an individual sample. Each row corresponds to a region of the consensus peak list. Normalized counts (DESeq2) from each sample are scaled per region. (b) Transcriptional start site enrichment (TSSe) scores for all ATAC-seq datasets. Datasets with TSSe > 15 were used for downstream analysis. Non-PAM rep2 was removed before downstream analysis. (c) Principal component analysis (PCA) of chromatin accessibility profiles in microglia from 5xFAD- (black) or 5xFAD+ mice (non-PAM: blue and PAM: red). Each symbol represents microglia isolated from one mouse. (d) Significantly enriched pathways of genes linked to DARs with increased chromatin accessibility in non-PAM compared to PAM.

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