An in vivo and in vitro spatiotemporal profile of human midbrain development (Supplementary Files)

Supplementary File 1: "inVitroLines_hg38LO.vcf"

VCF file with the donor genotypes of five iPSC-derived lines used for the in vitro dopaminergic differentiation and profiled with single-cell transcriptomics. This file is used for donor deconvolution with demuxlet, as the lines were pooled at the time of sequencing.  

200999750078_R05C02     ## Control 1
201464380013_R01C01     ## Patient 2
201464380013_R05C01     ## Crispr 1
202418170052_R06C02     ## Control 2
9934626012_R07C01       ## Patient 1

Supplementary File 2: "MLOallgenotypes.vcf.bgz"

VCF file with the genotypes of nine donors (5 iPSC-derived lines and 4 foetuses) that were profiled with single-cell transcriptomics.This file is used for deconvoluting the fetal data, as the lines were also pooled at the time of sequencing.  

200999750078_R05C02     ## Control 1
9934626012_R07C01       ## Patient 1
201464380013_R01C01     ## Patient 2
201464380013_R05C01     ## Crispr 1 (patient-corrected line from Patient 2)
202418170052_R06C02     ## Control 2
205437750120_R05C02     ## PCW16
205437750120_R06C02     ## PCW20
205794880025_R05C02     ## PCW12
205794880025_R06C02     ## PCW10

* The VCF file "inVitroLines_hg38LO.vcf" is a subset of the file "MLOallgenotypes.vcf.bgz", as it contains 5 out of the 9 donor genotypes. Still, as the initial donor deconvolution for the in vitro 10x libraries was performed with the subset we kept this file for reproducibility.

Supplementary File 3: "mlo_resolution075_Annot.RDS"

Single-cell data generated in our study (RDS object: Seurat object with counts and metadata).

Supplementary File 4: "midBrainIntegration.RDS"

Integrated datasets (RDS object: Seurat object with counts and metadata).