Extended data for manuscript "Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes" | Zenodo Skip to main Communities My dashboard Log in Sign up Published April 24, 2026 | Version v3 Dataset Restricted Extended data for manuscript "Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes" Authors/Creators Markowski, Julia (Researcher) 1, 2, 3 Kukalev, Alexander (Researcher) 4 Robens, Claudia (Researcher) Thieme, Christoph J. (Researcher) 4 Streck, Adam (Researcher) 5 Pombo, Ana (Project leader) 6, 4 Schwarz, Roland (Project leader) 5 Show affiliations 1. University of Potsdam 2.
Deutsches Institut für Ernährungsforschung 3. Harvard Medical School 4. Max Delbrück Center 5. University Hospital Cologne 6. Johns Hopkins University Description Resolving the three-dimensional structure of chromatin with haplotype specificity remains a fundamental challenge for understanding genetic and epigenetic contributions to gene regulation in healthy development and in disease. Phasing of chromatin contacts derived by ligation-dependent methods relies on high single-nucleotide variant (SNV) density, which limits its applicability in human genomes where SNVs are sparse. Here, we present CoPhasing, a strategy that leverages the intrinsic haplotype fidelity of Genome Architecture Mapping (GAM), a ligation-free method that inherently captures haplotype-matched genomic neighborhoods in thin nuclear slices. CoPhasing assigns SNV-free reads to their haplotype through proximity to informative reads, enabling efficient and accurate phasing even in SNV-sparse regions. Applying CoPhasing genome-wide reveals extensive,previously inaccessible structural heterogeneity between human homologous chromosomes, demonstrating the power of this approach to investigate allele-specific differences in 3D genome organization and their relevance to gene regulation and disease. This repository provides high-resolution cophased and nonphased segregation tables for the full set of SNPs F123 mESC GAM dataset and the results of the final permutation test results (differential contacts) for H1 hESC GAM dataset. Files Restricted The record is publicly accessible, but files are restricted. Log in to check if you have access. 99 Views 0 Downloads Show more details All versions This version Views Total views 99 42 Downloads Total downloads 0 0 Data volume Total data volume 0 Bytes 0 Bytes More info on how stats are collected.... Versions External resources Indexed in OpenAIRE Communities Details DOI DOI Badge DOI 10.5281/zenodo.19740137 Markdown [](https://doi.org/10.5281/zenodo.19740137) reStructuredText .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.19740137.svg :target: https://doi.org/10.5281/zenodo.19740137 HTML <a href="https://doi.org/10.5281/zenodo.19740137"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.19740137.svg" alt="DOI"></a> Image URL https://zenodo.org/badge/DOI/10.5281/zenodo.19740137.svg Target URL https://doi.org/10.5281/zenodo.19740137 Resource type Dataset Publisher Zenodo Rights License Creative Commons Attribution 4.0 International The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited. Read more Citation Export Technical metadata Created April 24, 2026 Modified April 24, 2026 Jump up About About Policies Infrastructure Principles Projects Roadmap Contact Blog Blog Support Help FAQ Developers REST API OAI-PMH Contribute GitHub Donate Funded by Powered by CERN Data Centre & InvenioRDM Status Privacy policy Cookie policy Terms of Use This site uses cookies. Find out more on how we use cookies Accept all cookies Accept only essential cookies