Single cell gene expression profiling of bone marrow derived DN thymocytes from wild-type or Bcl11b timing enhancer deletion (ΔTE) mice.

Removing the Bcl11b timing enhancer delays Bcl11b activation and results in decreased T cell output and increased ILC production in the thymus. We used single cell RNA sequencing (scRNA-seq) to analyze the transcriptional programs that are altered and lead to increased ILC generation in Bcl11b ΔTE mice. Bone marrow-derived DN1 (CD44+CD25-), DN2a (CD44+CD25+Bcl11b-), and DN2b (CD44+CD25+Bcl11b+) progenitors were FACS-purified from WT or ΔTE mice and re-cultured on OP9-DL1 stromal cells for four days before harvesting them for scRNA-seq.