X-omics iPSC data analysis workflow data and metadata files

Multi-omics dataset generated from induced pluripotent stem cells (iPSC) cultures, differentiated to neurons by Ngn2 transduction, for seven days. iPSCs were derived from three different patient groups [Myotonic Dystrophy Type 1 (DM1), chromodomain-DNA-helicase-binding protein 2 (CHD2) related disorder, and N-acetyl-d-neuraminic acid synthase congenital disorders of glycosylation (NANS-CDG)]. For each disease, cell lines from three patient donors (two females and one male) along with three controls were included. Cell lines were derived from fibroblasts or peripheral blood mononuclear cells (PBMCs) through lentiviral reprogramming into iPSCs. In addition, two isogenic lines using CRISPR-Cas9 were included: a CHD2-mutant line created by editing the control line 409B, and a corrected DM1 control line generated by removing the pathogenic repeat expansion from DM1 patient line 1. Three levels of replicates were defined. For some patients, multiple independent iPSC lines were used, which are referred to as clones. Moreover, each iPSC line was differentiated into neurons in three independent experiments and cultured for seven days in vitro by the same experimenter. These differentiation replicates will be referred to as the biological replicates in this study. Lastly, for specific analyses and specific omics data sets (proteomics & metabolomics) duplicate measurements on the same sample are available as well, which will be referred to as technical replicates. The multi-omics dataset included six omics layers from 44 samples: whole exome sequencing (WES), enzymatic methylation sequencing (EMseq), RNA sequencing (RNAseq), mass spectrometry (MS)-based proteomics, and untargeted MS-based metabolomics measured at two centers namely, the Radboud university medical center (RUMC) and the Leiden University Medical Center (LUMC), MS-based targeted and untargeted lipidomics.

1. http://publications.europa.eu/resource/authority/data-theme/HEAL

1. http://publications.europa.eu/resource/authority/language/ENG

1. https://fdp.radboudumc.nl/distribution/da97ab15-dc00-420b-a4b9-16b40662de49

1. http://data.europa.eu/eli/reg/2025/327/oj