REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Pooled dopaminergic differentiation	Jerber et al.8	HipSci Managed access (EGA: EGAS00001002885) HipSci Open Access (ENA: ERP121676)
Whole exome sequencing (WES) of HipSci lines	HipSci Project https://www.hipsci.org	HipSci Managed access: EGA HipSci Open Access (ENA: ERP006946)
HipSci genotype array data	HipSci Project https://www.hipsci.org Kilpinen et al.7	HipSci Managed access (EGA: EGAS00001000866, EGA: EGAS00001001272) HipSci Open Access (ENA: PRJEB11750)
Metadata for the dopaminergic differentiation single-cell dataset	This paper	https://zenodo.org/record/6079122#.YlSkxNPMJhE (Open Access)
Processed single-cell count (dopaminergic differentiation) for days 11, 30 and 52.	This paper	https://zenodo.org/record/6079122#.YlSkxNPMJhE (Open Access)
Macrophage differentiation	Alasoo et al.13	Table S1
Sensory neuron differentiation	Schwartzentruber et al.14	Table S1
Endoderm differentiation	Cuomo et al.15	EGA:EGAS00001002278 EGA: EGAD0001005741 ENA:ERP016000
Somatic mutations (acquired in vitro)	Rouhani et al.11	https://doi.org/10.1101/2021.02.04.429731
Software and algorithms
Variant effect predictor (VEP, release 99)	McLaren et al.49	https://www.ensembl.org/info/docs/tools/vep/index.html
BCFtools (version 1.4.25)	Danecek et al.50	https://samtools.github.io/bcftools/bcftools.html
Scanpy toolkit	Wolf et al.51	https://scanpy.readthedocs.io/en/stable/
Cellranger v3.1.0	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
R (4.0.4) / Bioconductor (3.12)	R Core Team, 2021 Bioconductor Project, 2021	https://www.r-project.org/ https://www.bioconductor.org/
Seurat (v4.0.1)	Butler et al.52	https://satijalab.org/seurat/
GOstats (v2.56)	Falcon and Gentleman53	https://bioconductor.org/packages/release/bioc/html/GOstats.html
Harmony	Korsunsky et al.54	https://portals.broadinstitute.org/harmony/articles/quickstart.html
Demuxlet	Kang et al.51	https://github.com/statgen/demuxlet
Other
Human reference genome NCBI build 37, GRCh37	Genome Reference Consortium	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Developmental disorder genes (DDG2P, version 2.2)	Wright et al.34	https://nhsgms-panelapp.genomicsengland.co.uk/panels/484/v2.2
Cosmic database (cancer-associated genes, version 90 – GRCh37)	Tate et al.35	https://cancer.sanger.ac.uk/cosmic
MSigDB hallmark gene set signatures	Liberzon et al.55	https://www.gsea-msigdb.org/gsea/msigdb/
1000 Genomes Project	The 1000 Genomes Project Consortium et al.56	https://www.internationalgenome.org/
Exome Aggregation Consortium 0.3.1	Lek et al.57	https://gnomad.broadinstitute.org/downloads
CADD Phred scores (version 1.6)	Rentzsch et al.58	https://cadd.gs.washington.edu/score
Original code (Zenodo)	This paper	https://doi.org/10.5281/zenodo.7641259 (Open Access, frozen repository)