RNA extraction and sequencing of iPSC-derived materials was performed using manufacturer's protocols for the RNeasy QIAcube kit on a QIAcube automated system (Qiagen). RNA sequencing libraries were generated, sequenced and analysed as described in the Supplementary material, ‘Methods’ section. Briefly, the data preprocessing was done with a custom Nextflow pipeline (https://github.com/wtsi-hgi/nextflow-pipelines/blob/rna_seq_5607/pipelines/rna_seq.nf), which includes the aligner parameters. Differential gene expression was analysed using the DESeq2 package44 (link) with SVA correction.45 (link) An adjusted P-value threshold of 0.05 was selected to identify significant differences between wild-type and mutant samples.
Other organizations :
PsiOxus Therapeutics (United Kingdom), Inserm, Université de Bourgogne, University of Cambridge, University of Maryland, Baltimore, Helen DeVos Children's Hospital, Corewell Health Blodgett Hospital, Spectrum Health, Alder Hey Children's Hospital, Liverpool Womens NHS Foundation Trust, University of Liverpool, University of Groningen, Institut de génétique et de biologie moléculaire et cellulaire, Erasmus MC, Leiden University Medical Center, University of Surrey, Clinic for Special Children, New Leaf Center, Eaton (United States), Oxford University Hospitals NHS Trust, London Health Sciences Centre, Western University, Children's National, Aarhus University Hospital, Leicester Royal Infirmary, Centre for Life
Bioinformatics pipeline for data preprocessing and analysis
controls
Positive control: Not specified
Negative control: Not specified
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