ATAC-seq data from DN3 and DN4 cells from WT, HEBcKO, and Rag2-KO mice

Gamma delta T cells that produce IL-17 (gdT17) play essential roles in barrier immunity and autoimmunity, but the gene networks that install their functions are not well understood. We have shown that the transcriptional regulator HEB is required for efficient upregulation of Id3 in response to TCR signaling in DN3 cells, and that Id3 is essential for maturation of gdT17 cells. To evaluate how the loss of the HEB affects chromatin status in response to TCR signaling, we compared thymocyte subsets from WT and adult HEB fl/fl Vav-iCre (HEB cKO) mice, which lack HEB in all hematopoietic cells, by ATAC-seq. We sorted DN3 and DN4 thymocytes from adult WT mice and HEB cKO mice. We also sorted DN3 cells from adult Rag2-/- mice, which cannot rearrange their TCR genes and thus are unable to develop beyond the DN3 stage.
, , Thymuses were dissected from adult Rag2-/-, WT, and HEB cKO mice, pressed through mesh to generate single cell suspensions, and incubated with Fc block. WT and HEB cKO DN cells were enriched by magnetic sorting using anti-CD4 and anti-CD8 microbeads according tothe manufacturer’s instructions (Miltenyi Biotech). Flow-through (CD4-CD8-) cells were stained and flow sorted into two populations: DN3 (CD4-CD8-CD44-CD25+) cells and DN4 (CD4-CD8-CD44-CD25-). DN3 cells were sorted from unfractionated Rag2-/- thymocytes, which do not develop past the DN3 stage. Duplicates were generated for each subset, with each replicate derived from three mice. The sorted cells were cryopreserved in aliquots of 100,000 cells each, which served as the input material for bulk ATAC-sequencing.
ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) is a method for determining chromatin accessibility across the genome. It utilizes a hyperactive Tn5 transposase to insert sequencing ad..., # ATAC-seq data from DN3 and DN4 cells from WT, HEBcKO, and Rag2-KO mice

Dataset DOI: [10.5061/dryad.4tmpg4fr5](https://doi.org/10.5061/dryad.4tmpg4fr5)

## Description of the data and file structure

These data revealed that E protein binding sites in the Id3 locus are accessible in DN3 cells from WT and Rag2-KO mice, and from DN4 cells in WT and HEB cKO mice.  However, DN3 cells from HEB cKO mice have dampened accessibility, indicating a role for HEB in remodeling of the Id3 locus prior to TCR signaling. 

Thymuses were dissected from adult Rag2KO  WT and HEB cKO mice, pressed through mesh to generate single cell suspensions, and incubated with Fc block. WT and HEB cKO DN cells were enriched by magnetic sorting using anti-CD4 and anti-CD8 microbeads according to the manufacturer’s instructions (Miltenyi Biotech). Flow-through (CD4-CD8-) cells were stained and flow sorted into two populations: DN3 (CD4-CD8-CD44-CD25+) cells and DN4 (CD4-CD8-CD44-CD25-). DN3 cells were sorted from unfr...,