H9 T2T assembly, sequence data

We present the first reference-quality diploid genome assembly of the human embryonic stem cell line H9 (WAe009-A), one of the most widely used pluripotent stem cell models in developmental and biomedical research. This cell line, registered in the European and NIH Human Pluripotent Stem Cell Registries, has verified ethical provenance, ensuring its transparent and responsible use for human pluripotent stem cell research. Using high-coverage Pacific Biosciences and Oxford Nanopore Technologies long-read sequencing, we generated a high-quality de novo assembly, phased it by integrating high-throughput chromosome conformation capture (Hi-C) data and validated it through multiple orthogonal methodologies. This assembly was coordinated by Simona Giunta of Sapienza University of Rome. PacBio HiFi and Hi-C sequencing was conducted by the Vertebrate Genome Lab (VGL) at the Rockefeller University, led by Erich D. Jarvis, Giulio Formenti, and Jennifer Balacco. ONT sequencing was conducted at the UC Santa Cruz Genomics Institute and Northeastern University. Genome assembly was completed by the VGL and Giunta Lab.