Fig. 4

Comprehensive Bursa Map of IBDV Infection Identified by Single-Cell RNA Sequencing. a Aggregated data of complete bursal cells separated based on normal (light brown) and virus-infected (dark brown) as represented by t-SNE clustering. b t-SNE distribution of normal and virus cells into nine sub-populations colored according to the unique cell cluster and transcriptional profiling. c t-SNE and Pie chart Quantification of nine major cells clusters. d Transcriptional profiling of complete single cells 42,484 associated with nine major clusters shown in the column. Gene expressions of each specific cluster are shown for specific genes in rows. The gene expression matrix displays each clustering of cells based on different treatments (yellowish/light brown respectively for each cluster on the top of the heat map). e t-SNE and pie distribution of whole cell population into five different immune and non-immune cell types shown in t-SNE and unique coloured difference. f Heat map of transcriptional profiling of whole single cells into five major immune and non-immune cells shown in the column. Gene expressions of each cell type are shown for specific genes in rows. The gene expression matrix displays each clustering of cells based on expression level (yellowish/light brown respectively for each cell type on the top of the heat map). g and h Cells are also gated for Bu1 (B cells marker), CD45 (leukocytes and hematopoietic cell marker), CD4 + T cells, and MHCII, and the quantification for FACS are shown for each marker (green represent control and red represent infected) in each group. n = 4 from 3 chickens per group. All data shown are the mean results ± SD, and statistical significance was determined using one-way ANOVA. Significance difference was expressed as, *p < 0.05, ****p < 0.0001