Gene expression analysis of WT and Stat1-/- CD4+ T cells pre and post transfer into Rag1-/- mice

To understand the basis behind the defective survival/expansion of Stat1-/- CD4+ T cells in Rag1-/- mice, we analyzed the gene expression of WT and Stat1-/- CD4+ T cells pre- and post-transfer into these mice by RNAseq. WT (C57BL/6) or Stat1-/- CD4+ T cells (3 donor mice/group) were MACS sorted by negative selection. Some of the T cells from each mouse was used for RNAseq (Pre-transfer, WT=1, KO=2). The remaining T cells were injected into Rag1-/- mice (5 mice/group) and FACS sorted from the spleens and lymph nodes (CD45+ CD3ε+ CD4+) 7 days later. In the post-transfer setting, the T cells from the 5 mice of each group were split into 3 biological replicates each containing 1-2 mice (denoted as WT or KO).