mdc = muscle[muscle.obs.annotation == 'DC-migratory'].copy()

mdc = mdc.raw.to_adata().copy() mdc.raw = mdc.copy()

sc.pp.highly_variable_genes(mdc, max_mean=10) sc.pp.scale(mdc) sc.tl.pca(mdc, use_highly_variable=True)

sc.pp.neighbors(mdc) sc.tl.umap(mdc)

scl.us(mdc, 'treat')

sc.tl.leiden(mdc,0.3)

scl.us(mdc, 'leiden')

mdc = mdc[~mdc.obs.leiden.isin(['3'])].copy()

mdc = mdc.raw.to_adata().copy() mdc.raw = mdc.copy()

sc.pp.highly_variable_genes(mdc, max_mean=10) sc.pp.scale(mdc) sc.tl.pca(mdc, use_highly_variable=True)

sc.pp.neighbors(mdc) sc.tl.umap(mdc)

scl.us(mdc, 'treat')

sc.tl.leiden(mdc,0.2)

scl.us(mdc, 'leiden')

mdc.obs['anno'] = mdc.obs['leiden'].astype(str).map({'0':'mDC_others','1':'mDC_ISG'})

sc.write("data/mDC_230504.h5ad", mdc)

ISG+ and related DCs

image.png https://pubmed.ncbi.nlm.nih.gov/34800368/

image.png https://doi.org/10.1016/j.immuni.2020.04.005