GSE110722
Genome-wide maps of chromatin state in naïve CD4+ T cells and WT/EZH2-null TFH and TH1 cells
ATAC-Seq experiments were performed to elucidate the chromatin state changes among naïve CD4+ T cells, WT follicular helper T (TFH) cells and WT type 1 helper T (TH1) cells. The analysis suggested stringent lineage-specific mode of chromatin accessibility in each group, indicating chromatin remodeling is tightly associated with TFH versus TH1 lineage differentiation in response to acute viral infection. Furthermore, the comparison between wild-type and EZH2-null TFH cells showed that less-opening state of certain chromatin accessible region in TFH-differentiation associated genes in the formers, suggesting EZH2 led to permissive chromatin accessibility primarily at specific regions of TFH-associated genes. Overall design: WT and EZH2-null TFH and TH1 cells at day 8-post LCMV Armstrong infection, and naïve CD4+ T cells were sorted (2 samples per group, each sample was pooled from at least 5 mice). The ATAC-Seq libraries of the sorted cells were then prepared by using the Nextera DNA Sample Preparation Kit (FC-121-1030, Illumina), followed by sent to next generation sequencing. Please note that [1] the strain of the mice used is a hybrid of C57BL/6 (CD4 Cre) and 129 SV (Ezh2 fl/fl), and [2] each processed data was generated from both replicate samples combined and is linked to the corresponding rep1 sample records.