H9 ancestry analysis
Ancestry
Scaffold lengths
Scaffold lengths

This site provides genome data and a UCSC Genome Browser track hub for the telomere-to-telomere (T2T) haplotype-resolved diploid assembly of the H9 (WAe009-A) human embryonic stem cell line. The hub includes gene annotations (CAT consensus genes, miRNAs, and tRNAs), multi-lab H9 RNA-Seq datasets, methylation and ATAC-seq tracks, Hi-C compartments, repeat and segmental duplication annotations, and whole-genome alignments to T2T-CHM13 and GRCh38. H9-specific genomic features are well-represented, including telomere annotations, CENP-B boxes, and variants linked to pluripotency and neurodevelopmental phenotypes.

βš—οΈ The T2T-H9 Hub is under development. More tracks, including multiple alignments, and better documentation will be available soon.

πŸ”— UCSC Browser hub links

🧬 Genome annotation files

  1. haplotype 1 CAT genes V2
  2. haplotype 2 CAT genes V2

πŸ“¬ Contact us

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πŸ“„ Citation

The diploid reference genome of a human embryonic stem cell line. he diploid reference genome of a human embryonic stem cell line Ivana Pacar, Matteo Tommaso Ungaro, Ying Chen, Hamza Dallali, Jack A. Medico, Prajna Hebbar, Mark Diekhaus, Elena Di Tommaso, Margarita Geleta, Patricia P. Chan, Todd M. Lowe, Jennifer Balacco, Nivesh Jain, Francine Ackerman, Michela Mochi, Alexander G. Ioannidis, Niranjan Sawarkar, Kasandra Diaz, Kavitha Krishna Sudhakar, Joseph E. Powell, Miten Jain, Alessandro Rosa, Gist F. Croft, Andrea Tanzer, Erich D. Jarvis, Giulio Formenti, Sofie R. Salama, Simona Giunta bioRxiv 2026.03.26.714432; doi: 10.64898/2026.03.26.714432
Ivana Pačar, Mark Diekhans