Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• The genetic basis for DNA methylation variation across tissues and development.

  PMID 41980926 · PMC13254082 · Nature communications · 2026 · 8 claims · 8 setups

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  Strain-specific DMRs between mouse strains are associated with nearby sequence polymorphisms that disrupt TF binding motifs

  cerebellum liver embryo ctcf rrbs wgbs motif

• Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

  PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

  Has reproduction

  SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

  dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial

• Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

  PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

  Has reproduction · 95

  Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

  embryonic escs dem-cgis demg methylation chip-seq gene

• DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency.

  PMID 31722211 · PMC6856714 · Cell reports · 2019 · 7 claims · 6 setups

  Has reproduction · 50

  The altered 3D genome of 2i-cultured ESCs (chromatin decompaction and loss of polycomb interactions at polycomb targets) is due to redistribution of polycomb away from its targets.

  ring1b− e3.5 e14 3b3l fluorescence fish situ

• H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity.

  PMID 40764058 · PMC12487818 · Genome research · 2025 · 8 claims · 8 setups

  Has reproduction · 55

  H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding

  imefs early ctcf h3k9me3 h3k9me2

• A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration.

  PMID 41840725 · PMC13104449 · Human genomics · 2026 · 7 claims · 8 setups

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  Multi-omics consensus clustering (MOVICS) identifies two distinct SKCM molecular subtypes, CS1 and CS2

  tcga-skcm meta-geo gtex melanoma multi-omics bulk transcriptome-wide

• Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

  PMID 41578129 · PMC12932634 · NPJ breast cancer · 2026 · 8 claims · 7 setups

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  Identified 30 isolated tumor cells (ITCs) in a clinically metastasis-negative tumor-draining lymph node, representing the initial metastatic seeding event, spanning ~200 μm

  dissected same tumor xenium-derived bulk enzymatic whole-genome

• Unraveling the histone's potential: a proteomics perspective.

  PMID 18849650 · PMC2662511 · Epigenetics · 2008 · 8 claims · 8 setups

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  Mass spectrometry can determine the full repertoire of histone PTMs, their residue-specific location, and combinatorial patterns without requiring prior knowledge of the modification, unlike antibody-based methods

  histone overexpressed lysate top-down middle-down quantitative

• Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.

  PMID 41634861 · PMC12955163 · Genome biology · 2026 · 8 claims · 8 setups

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  PHap is a new pipeline that enables haplotype-resolved, near-T2T assembly of autopolyploid genomes using only standard HiFi, ONT-UL, and Hi-C sequencing data

  autotetraploid parental huashu4 pacbio hi-c illumina