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. 2019 Mar 6;17(3):247–260. doi: 10.1038/s41423-019-0219-z

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — Chromatin states of the virus-specific T_FH and T_H1 cells in response to an acute viral infection. a Numbers of chromatin peaks with differential accessibility (FDR < 0.05; FC > 4) between SMARTA T_FH cells and SMARTA T_H1 cells at the indicated time points after LCMV Armstrong infection. b PCA plot of the peak accessibilities in naïve SMARTA CD4⁺ T cells, SMARTA T_FH cells (days 2, 5 and 8 postinfection) and SMARTA T_H1 cells (days 2, 5 and 8 postinfection). Each dot represents a replicate of the indicated group. c Chromatin accessibility heat map of differential peaks from a. Each row represents one of the 15,600 differential peaks that was center-aligned and extended upstream and downstream by 1 kb from the center. The peaks are K-means clustered. d ATAC-Seq signal profiles of T_FH lineage-associated gene loci. e ATAC-Seq signal profiles of T_H1 lineage-associated gene loci. Differential peaks are highlighted in gray (d and e). The data were obtained from one experiment with three biological replicates (pooled from at least five mice per group) (a–e)