- I get the list of cell type markers during mouse gastrulation from
Pijuan-Sala
et al. 2018 interactive atlas. From “cell-type markers”, I download
the list of marker genes with FDR < 0.1 for various cell types
detected at the following stages:
- E6.5 (all cell types)
- E6.75 (all cell types)
- E7 (all cell types)
- E7.25 (some cell types appearing at this stage)
- E7.5 (some cell types)
- I remove all markers which are not unique for one cellType-cellStage
combination.
- I filter out all markers with rowMean < 10 among all epiblasts
samples in my dataset.
- I compute the average expression of the markers belonging to each
cellType-stage combination, including E7 nascent mesoderm, which I
select as the most indicative considering GSEA result and the stage of
dissection.
- I compute the average expression of the two de-novo DNMTs (Dnmt3a
and Dnmt3b) and Tet1 enzymes.
- Scatterplot of 4 vs 5.
