RNA-sequencing of mouse double-negative developing thymocytes [CD4-, CD8-, CD3-, B220-, CD25high, CD44low, and CD117low]

We performed a transcriptome comparison of double-negative developing thymocytes from the DN3 population, differing in their CD27 and CD28 expression Double-negative developing thymocytes were gated for CD4-, CD8-, CD3-, B220-, CD25high, CD44low, and CD117low expression, which define the DN3 stage of thymocyte development. Within this population, cells were separated in 3 groups based on their CD27 and CD28 expression (DN3a CD27low CD28low, DN3a CD27high CD28low, and DN3b CD27high CD28high) that were pooled for bulk RNA-sequencing. The experiment was performed in four replicates, giving a total of 12 samples.