DNA Methylation Analysis of Human-Mouse DNA Mixtures for Xenograft Models

A 3.3 MB dataset from figshare, last updated April 30, 2026, by author Takahiro Ebata. It contains results from DNA methylation microarray analysis using the Infinium MethylationEPIC v2.0 kit. The data was generated to establish a method for minimizing the effect of mouse DNA contamination in human samples from cell line and patient-derived xenograft models.

Use Cases

• Filtering low-reproducibility and cross-reacting probes based on the identified 7,446 and 133,377 probe sets mentioned in the description
• Improving correlation analysis of methylation levels in contaminated human DNA samples using the described functional probes
• Validating DNA methylation analysis methods for cell line xenograft (CDX) and patient-derived xenograft (PDX) models
• Benchmarking bioinformatics pipelines for handling species contamination in epigenetic datasets

Strengths

• Includes analysis of 7,446 low-reproducibility probes and 133,377 mouse cross-reacting probes, providing specific filtering targets
• Method validated on both pure DNA mixtures and cell line xenograft (CDX) samples from RKO and Pa-Tu-8902 cell lines
• Dataset is openly licensed under CC-BY-4.0 for reuse and modification

Limitations

• Column-level documentation is absent; field semantics must be inferred after download
• Row count is unknown, which may limit suitability assessment
• Data files are in XLSX and PPTX formats, which may require specific software for access

Provenance

Source

figshare

Collection Method

Generated by mixing fully methylated and unmethylated human DNA from HCT116 cell line with fully methylated mouse DNA, then analyzed using Infinium MethylationEPIC v2.0 kit.

Time Range

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Freshness

Last updated 2026-04-30 08:40:03; freshness should be verified

Geography

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