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. 2020 Aug 7;8(2):e001053. doi: 10.1136/jitc-2020-001053

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© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.

This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See http://creativecommons.org/licenses/by-nc/4.0/.

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Transcriptome analysis of CD163⁺ cDC2 cells. CD5⁺CD14^‒CD163⁺ DC and CD14⁺CD163⁺ were isolated by flow activated cell sorter (FACS) sorting and analyzed by bulk RNA sequencing as described.14 (A) Heatmaps displaying median log2-transformed TPM + 1.0 expression values of genes associated with CDC phenotype, HLA, TNF/TNFR superfamily, cytokine and chemokine (receptor) activity, toll-like receptor (TLR) binding and TNF and IFN signaling within CD163⁺ cDC2 cells. (B) Volcano plot showing differential gene expression between CD14⁺CD163⁺ and CD14^‒CD163⁺ cells. Gene expression data are depicted as log2(Fold change) versus –log10(false discovery rate (FDR)). P values were calculated using DESeq2. (C) Ingenuity pathway analysis of differentially regulated genes (<0.05 FDR) between CD14⁺CD163⁺ and CD14^‒CD163⁺ cells displayed as a histogram plot showing the −log10 (p value) and the Z score for each pathway using twofold upregulated and downregulated DEGs of each subset. cDC2, conventional dendritic cell type 2; DEGs, differentially expressed genes; TPM, transcript per million.