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[Preprint]. 2023 Jan 24:2023.01.24.525203. [Version 1] doi: 10.1101/2023.01.24.525203

Figure 2: Celltype-specific chromatin accessibility dynamics in response to vaccination.

Figure 2:

(A) Bridge integration-based mapping of human PBMC scATAC-seq data onto the CITE-seq dataset from Figure 1B, using a multi-omic dataset as a bridge. Cells are colored by reference-derived annotation. (B) Coverage plots indicating chromatin accessibility around IFI6, IFITM3, and ISG15 in CD14 monocytes across all time points. Corresponding gene expression for each cell population, from the CITE-seq dataset, is shown on the right. (C) Scatter plot measuring correlation between Day 0 and Day 2 pseudo-bulk chromatin accessibility of CD14 monocytes. Each point corresponds to a called scATAC-seq peak. (D) UMAP visualization of scATAC-seq data on Day 0 and Day 28 after bridge integration. Vaccine-induced populations are highlighted in red. (E) CD38 protein expression levels, which were not considered during the bridge integration procedure, are correctly up-regulated in cells predicted to be vaccine-induced. (F) Examples of enhancer loci that are specifically accessible in vaccine-induced cells. Chromatin accessibility patterns on Day 28 are shown for four selected cell types. SNP sites are annotated as yellow lines. (G) Motif-based overrepresentation analysis of transcription factor binding sites in the top 1000 peaks with differentially enriched accessibility in the vaccine-induced group A cells.