RNA-sequencing data from Ctrl (Id2F/F or Id2F/FTcf7F/F), Ncr1Cre Id2F/F, Ncr1Cre Tcf7F/F and Ncr1Cre Id2F/F Tcf7F/F bone marrow NK cells.

The goal of this study was to determine how gene expression changes when Id2 and Tcf7 are deleted in bone marrow natural killer cells as compared to NK cells in which only Id2 or Tcf7 are deleted. We sorted NK1.1+CD49b+ cells from the bone marrow of mice with each of the indicated genotypes. Reads were aligned to the mm10 reference genome by Tophat2.1.0. Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78. Differential expression was calculated across 3 independent replicates by EdgeR. We found that NK cells lacking Id2 had reduced expression of mature NK cell genes and increased expression of immature genes and known E protein target genes. Deletion of Tcf7 in ID2-deficient NK cells partially restored expression of maturation associated genes and decreased immature genes bringing their gene expression profiles closer to that of Ncr1Cre Tcf7F/F or Ctrl NK cells. Overall design: Expression profiling analysis by RNA-sequencing of bone marrow NK1.1+CD49b+ natural killer cells in Ncr1Cre Id2F/F, Ncr1Cre Tcf7F/F or Ncr1Cre Id2F/F Tcf7F/F mice. Id2F/F or Id2F/FTcf7F/F bone NK cell were used as controls . 3 independent replicates per sample.