Nature Research Reporting Summary.pdf

- Study Design (Life Sciences):
- Sample size: Based on previous human eQTL studies, with power increasing with sample size (100-200 samples).
- Data exclusions: Single-cell RNA-seq data excluded based on quality control criteria.
- Replication: Main dataset replicated across 19 experiments, with some failed differentiation assays. Identification of a subpopulation replicated in an independent dataset.
- Randomization: iPSC lines allocated to groups/experimental batches at random.
- Blinding: Investigators blinded during collection, origin of assayed cells determined during data analysis.

- Materials & Methods:
- Relevant to the study: Antibodies, eukaryotic cell lines (iPSCs from the HipSci project), human research participants.
- Antibodies used: Validated commercially available antibodies for FOXA2, LMX1A, TH, MAP2, and corresponding secondary antibodies.
- Cell lines: All iPSCs from the HipSci project, matched to original donors by genotype using RNA-sequencing data. Not tested for mycoplasma contamination.
- Human research participants: 25 to 79 years old phenotypically 'healthy' donors (male and female) with no diagnosed genetic disease.

- Data & Software Availability:
- Managed access data: European Genome-phenome Archive (EGA) under study number EGAS00001002885.
- Open access data: European Nucleotide Archive (ENA) under study ERP121676.
- Processed data and eQTL summary statistics: Zenodo (https://zenodo.org/record/4333872).
- Software: Combination of NGS analysis tools, CellRanger, STAR, GATK, demuxlet, R (Harmony, MNN), and Python (Scanpy). Unpublished scripts available at https://github.com/single-cell-genetics/singlecellneuroseqpaper/.