Fig. 4: Single-cell transcriptome sequencing characterized cellular and molecular changes of peripheral blood mononuclear cells (PBMCs). | Nature Communications

Fig. 4: Single-cell transcriptome sequencing characterized cellular and molecular changes of peripheral blood mononuclear cells (PBMCs).

From: Long-term effects of Omicron BA.2 breakthrough infection on immunity-metabolism balance: a 6-month prospective study

Fig. 4

a UMAP graph displays the cell types and clustering of PBMCs. Firstly, the Azimuth algorithm is used to map the data to the reference cell set of PBMC, and then combined with specific high expression genes to manually determine the cell type. b UMAP graph shows cell types and clustering of PBMCs in control and BA.2-BTI-6m groups. c Dotplot diagram with marker genes corresponding to different cell types. Naive CD4 T cells (CD4T Naive) (CD3D/CD4/CAMK4/LTB/SELL/TCF7/CCR7), Central memory CD4 T cells (CD4 TCM) (CD3D/CD4/CAMK4/IL7R/IL6ST), Effector memory CD4 T cells (CD4 TEM) (CD3D/CD4/CAMK4/IIFI44/GZMK/OASL), Regulatory T cells (Treg) (CD3D/CD4/CAMK4/FOXP3/IL2RA), Naïve CD8 T cells (CD8T Naive) (CD3D/CD8A/CD8B/LTB/SELL/TCF7/CCR7), Central memory CD8 T cells (CD8 TCM) (CD3D/CD8A/CD8B/NELL2/LYAR), Effector memory CD8 T cells (CD8 TEM) (CD3D/CD8A/CD8B/ IFIT2/GZMH/CCL5), Mucosal-associated invariant T (MAIT) cells (KLRB1/SLC7A5), γδ T cells (gdT) (TRGV9/TRDV2), natural killer (NK) cells (GNLY’/KLRD1), B cells (CD79A/MS4A1), CD14 monocyte (LYZ/S100A8/S100A9/CD14), CD16 monocyte (LYZ/FCGR3A/LST1), IL1B+ monocyte, HOOK2+ monocyte, dendritic (DC) cells (CST3/HLA-DQA1/CSTA), plasmacytoid dendritic (pDC) cells (IGKC/JCHAIN/PLD4) and platelet (PLTs) (NRGN/PPBP). d Stacked bar charts display the proportion of different cell types in a single sample. e UMAP plot shows differences in cell composition between control and BA.2-BTI-6m groups identified based on Milo algorithm. f The figure shows the fold change of cell composition in the control and BA.2-BTI-6m groups identified based on Milo algorithm. g Number of differentially expressed genes in different cell types in the control and BA.2-BTI-6m groups. h Bubble chart displaying biological functions enriched by significantly upregulated genes in different cell types. i Bubble chart displaying biological functions enriched by significantly downregulated genes in different cell types. P value is calculated through hypergeometric testing and adjusted by the Benjamin and Hochberg methods.

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