Region-level 5mC/5hmC methylation and 8-oxo-dG profiles from nanopore sequencing of palmitate-treated human adipose-derived mesenchymal stem cells

Abstract

Processed, region-level data supporting the article "Lipotoxic Palmitate Hyperpolarizes Mitochondria, Raises 8-oxo-dG Damage in Depleted mtDNA, and Converts Nuclear 5mC to 5hmC Genome-Wide in Human Adipose-Derived Mesenchymal Stem Cells" (International Journal of Molecular Sciences, submitted 2026). Human adipose-derived mesenchymal stem cells (one commercial lot) were left untreated (NT) or exposed to 250 µM sodium palmitate (PA) for 24 h. Native DNA of each arm was sequenced on an Oxford Nanopore R9.4.1 flow cell and aligned to T2T-CHM13v2.0. 5mC was called with Guppy 5.0.16 and the Rerio all-context model (threshold 0.70), 5mC and 5hmC with dorado 0.9.6 (5mCG_5hmCG@v0) on a 10% read subset, and 8-oxo-dG with esox. Files (tab-separated; .tsv.gz = gzip-compressed table; full column descriptions in README.md): Methylation profiles (pooled % 5mC = modified / valid calls per region) • methylation_summary_region_classes.tsv — % 5mC NT and PA and their ratio for CpG islands, shores, shelves, promoters, exons, gene bodies and the whole genome. • methylation_profile_cpg_islands.tsv.gz — one row per CpG island (28,667): coordinates, number of CpG on the reference, % 5mC NT and PA, ratio. • methylation_profile_promoters_tss1kb.tsv.gz — the same per promoter, TSS ± 1 kb (19,134 genes). • methylation_profile_gene_bodies.tsv.gz — the same per gene body (19,134 genes). • methylation_profile_gene_panels.tsv — the same for five pre-specified gene panels (adipokines, oxidative damage and redox, mitochondrial and metabolic, ageing and senescence, innate immunity). • methylation_IL1B_production_axis.tsv — IL-1β production-axis genes at five genomic scales. • methylation_per_read_beta_distribution.tsv — distribution of reads by their own methylation fraction. • methylation_by_repeat_class.tsv — % 5mC per RepeatMasker class. • methylation_metagene.tsv — % 5mC along a scaled gene, 2 kb upstream to 2 kb downstream. 5mC and 5hmC • methylation_5mC_5hmC_genome_wide.tsv — 5mC and 5hmC calls and percentages per arm. • table_S3_5mC_5hmC_by_read_quality.tsv, table_S4_5mC_5hmC_by_quality_decile.tsv, table_S5_5mC_5hmC_ribosomal_DNA.tsv — Supplementary Tables S3–S5. 8-oxo-dG • oxidation_8oxodG_rates_by_compartment.tsv — rate per million callable guanines with 95% interval: mitochondrial DNA, nuclear gene panel, ribosomal DNA. • oxidation_8oxodG_ratios_by_compartment.tsv — palmitate-to-untreated ratios of the same compartments. • oxidation_8oxodG_by_sequence_context.tsv — calls and opportunity per trinucleotide context. • oxidation_8oxodG_by_molecule_methylation_tertile.tsv — 8-oxo-dG rate in molecules grouped by their own methylation. • methylation_around_8oxodG_profiles.tsv — mean 5mC score of CpGs at 1–1000 bp from 8-oxo-dG anchors and from ordinary guanines on lesion-carrying and lesion-free molecules (50 bp bins). Run summary • table_S2_sequencing_run_summary.tsv — reads, bases, read length, quality and coverage (Supplementary Table S2). • README.md, MD5SUMS. Per-region files exclude chrX, chrY and the mitochondrial genome. Raw signal, reads, alignments and per-site or per-read tables are not included because they contain the genetic information of the cell donor (Regulation (EU) 2016/679, Art. 9); they are available from the corresponding authors on reasonable request under a data use agreement. Analysis code: https://github.com/SoryHay/admsc-palmitate-8oxoG-methylation.