RNA-seq of CD4 CD8 lineage differentiation in the mouse thymus

We used flow cytometry to sort phenotypically defined thymocyte populations and profiled gene expression by paired end RNA-sequencing. We used CD4, CD8, CD69 and TCRbeta cell surface markers to sort phenotypically defined thymocyte populations by flow cytometry from the thymi of 6 weeks old mice on a mixed C57BL/6 and 129 background. Populations include CD69neg pre-selection DP thymocytes, CD4 and CD8 SP thymocytes, and a series of selection intermediates (CD69pos DP, TCRhigh DP and CD4pos CD8low). We profiled gene expression by paired end RNA-sequencing.