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).
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Has reproduction · 80
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.
PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups
BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules
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Has reproduction
Pleiotropic effects of MORC2 derive from its epigenetic signature.
PMID 40302207 · PMC12782172 · Brain : a journal of neurology · 2026 · 8 claims · 8 setups
A MORC2-specific DNA methylation episignature exists that is universal across all MORC2-associated phenotypes and conserved across blood and fibroblast tissue
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Has reproduction · 95
Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.
PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups
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.
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Has reproduction · 58
Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).
PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups
A cheetah-specific epigenetic age clock using 52 CpG sites predicts chronological age across blood and liver with r=0.97 and MAE=0.86 years
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Has reproduction · 55
H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity.
PMID 40764058 · PMC12487818 · Genome research · 2025 · 8 claims · 8 setups
H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding
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Has reproduction
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.
PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 8 claims · 5 setups
The nasal methylome shows differential DNA methylation in intergenic regions and low methylated regions (LMRs), highlighting distal regulatory/enhancer-like elements in COVID-19 gene regulation
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Full-text index only
Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a.
PMID 18096052 · PMC2246272 · Genome biology · 2007 · 6 claims · 4 setups
Suv39h1 and G9a associate with previously reported methylation states (Suv39h1 with H3K9me3; G9a with H3K9me/me2)
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Has reproduction · 73
Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use.
PMID 37218167 · PMC10208159 · Epigenetics · 2023 · 8 claims · 7 setups
Probe-specific upper and lower thresholds for flagging aberrant DNA methylation can be derived from a reference database of >2,000 normal and tumour-adjacent normal samples spanning 25 tissue types.
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Has reproduction · 63
A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.
PMID 30332484 · PMC6192621 · PloS one · 2018 · 7 claims · 8 setups
The CGCG element (consensus TCTCGCGAGA) is a conserved 10-bp motif enriched in TATA-less, CpG island-associated promoters of ribosomal protein and housekeeping genes.
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Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
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Has reproduction · 71
A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.
PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups
MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples
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Has reproduction · 100
msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data.
PMID 36123620 · PMC9487059 · BMC bioinformatics · 2022 · 6 claims · 8 setups
msPIPE is a new end-to-end pipeline integrating pre-processing, alignment & methylation calling, and downstream DNA methylation analysis (profiling, HMR, DMR, functional enrichment) with publication-quality figure output for WGBS data
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Has reproduction · 74
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups
MicroPIPE, an end-to-end Nextflow/Singularity-based pipeline built from systematically validated tool choices, produces high-quality complete bacterial genome assemblies without manual intervention.