search

chenweng1991 / redeem_reproducibility

Analysis reproducibility of Weng et al paper "Deciphering cell states and genealogies of human hematopoiesis"
2 stars 1 forks source link

Refined HSC cluster #3

Open danielee0707 opened 6 months ago

danielee0707 commented 6 months ago

Hello, I have a question about the cell type annotations. When I checked the Young1.All.T1 Seurat object you shared on figshare, there is a cluster called Refined.HSC in STD.CellType field, which appears in both DN4_HSC dataset and DN4_HSPC dataset, but the UMAP plot in Fig2c does not contain this cluster. Was it renamed to something else during plotting?

chenweng1991 commented 5 months ago

Dear @danielee0707 : Thanks for your question! The refined.HSC are more carefully defined HSCs that are used in Fig3, and Fig4 for HSC focused analysis. The rationales for defining are described in Methods. The majority of refined HSC are from the HSC datasets, but there are also some from DN4_HSPC. Basically it is a more stringent definition for HSCs than the one plotted on Fig2.

Best regards Chen