An in vivo and in vitro spatiotemporal atlas of human midbrain development (Supplemental Data)

Supplemental data for the pre-print "An in vivo and in vitro spatiotemporal atlas of human midbrain development". It includes:

Data S1: "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 1201464380013_R01C01     ## Patient 2201464380013_R05C01     ## Crispr 1202418170052_R06C02     ## Control 29934626012_R07C01       ## Patient 1

Data S2: "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 19934626012_R07C01       ## Patient 1201464380013_R01C01     ## Patient 2201464380013_R05C01     ## Crispr 1 (patient-corrected line from Patient 2)202418170052_R06C02     ## Control 2205437750120_R05C02     ## PCW16205437750120_R06C02     ## PCW20205794880025_R05C02     ## PCW12205794880025_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.

Data S3: "mlo_resolution075_Annot.RDS"

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

Data S4: "midBrainIntegration.RDS"

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