In silico isolation of E16.5 Rag1 knockout thymic hematopoietic cells

For whole-thymus samples from Rag1 knockout embryos, the same alignment, quantification, and quality control steps were performed (>1000 genes per cell, >3 cells per gene). Cells were classified by k-nearest-neighbors (k = 25) after projection into a 20-dimensional principal subspace, with both PCA and classifier trained on the E12.5-E16.5 wild-type data. Cells classified into any of the six thymic hematopoietic cell clusters were retained for analysis.