[ ] what differentiates the NCR3+ early cells from CD52+ early cells? Expression of NCR3 is low before 8 pcw. Could it be an organ specific effect? Try fitting gene expression to time
[ ] Check early to late differences in thymic DPs
[ ] generate systematic DGE for early VS late cells in cell types with > n neighbourhoods with opposite direction, send to Isaac for summarisation
Factor analysis for differences within cell types
[ ] organ specific differences in pro B cells
[ ] TH t cells vs other: do we see naiveness on one side and activation on the other?
[ ] organ specific differences in all B cell progenitors
[ ] Define significant connectivity values using a permutation test
misc
[x] re-embedding of ILCs including 5' data (KNN smoothing of velocity latent time)
[ ] Are ribosomal genes differentially expressed in many subsets?
AIF1: B cell survival factor, chemotactic
[x] check other subsets where AIF1 is differentially expressed
Notable in NK late: the chemokines (the ligands and not the receptors), CD69 (tissue residency marker), interferon, granzyme respone (active NK), CD45/CD7 lymphocyte lineage (more immature phenotype?)
[ ] cellphoneDB-like analysis of expression of receptors of ligands produced by late NK cells
LI-HSC
[x] check MIF
[ ] Show that switch in proportion of HSCs from liver and bone marrow coincides with switch in expression of lymphoid priming markers
Differential abundance analysis on NK cells
Factor analysis for differences within cell types
misc