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Teichlab / Pan_fetal_immune

Collection of scripts for analysis of pan fetal immune atlas

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Closed emdann closed 2 years ago

emdann commented 3 years ago

Differential abundance analysis on NK cells

[ ] 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)

emdann commented 3 years ago

TO DO:

emdann commented 3 years ago

Differential abundance analysis

[x] Sanity check on FACS correction: test in unsorted cells only and compare effects
[ ] Differential abundance test on cell type labels (once I have the labels)
[x] Figure with lines of first emergence of cell types (w cufoff of min number of cells, see JP review)

Unproductive TCR expression

emdann commented 3 years ago

Feedback on early/late populations DGE analysis:

[ ] 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