Midbrain organoid single-cell scanpy objects

Unbiased single-cell RNAseq of Day 49 midbrain dopaminergic organoids (10x 3') of the Patikas et al. publication.

The model-dataset.h5ad refers to the object shown at Fig 2A and contains 3 cell lines: 

KOLF2 ( Control cell line)

SNCA-3x alpha Synuclein triplication Parkinson's Disease patient-derived iPSC line

SNCA-corr (SNCA-3x isogenic control with the triplication mutation corrected)

The full-dataset.h5ad refers to the object shown at Fig 4 onwards and contains the 3 cell lines that are included in model-dataset.h5ad and 7 other single-cell RNAseq samples: 

SNCA-3x+KOLF2 (chimera organoid condition of SNCA-3x and KOLF2 of iPSCs grown together in a midbrain organoid)

SNCA-corr+KOLF2 (chimera organoid condition of SNCA-corr and KOLF2 of iPSCs grown together in a midbrain organoid)

5 paired rotenone conditions. For each condition (KOLF2, SNCA-3x, SNCA-corr, SNCA-3x+KOLF2, SNCA-corr+KOLF2) a paired condition with acute 24h rotenone treatment in an antioxidant-free medium.