cc-by-4.0Budinger, DimitriPuigdevall Costa, PauHall, George T.Charlotte, RothXenakis, TheodorosMarrosu, Elenajerber, julieDi Domenico, AlessandroKilpinen, HelenaCastellano, Sergibarral, serenaKurian, Manju Ann2025-03-242024-09-152024-09-15https://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/10915Supplemental 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).     Opendataset