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).

Publications 1.3k Datasets 392.5k Experiments 51

System / cell line: specific ✕ Assay: methylation ✕ Clear

High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer.

PMID 16432260 · PMC1345698 · Nucleic acids research · 2006 · 8 claims · 5 setups

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A 96-well high-throughput bisulfite modification (HTBM) method was developed and validated against single-sample bisulfite modification (SSBM), producing comparable methylation results even from as little as 3 ng DNA.

genomic normal advanced bisulfite-treated methylation-specific bisulfite snp
Non-imprinted allele-specific DNA methylation on human autosomes.

PMID 19958531 · PMC2812945 · Genome biology · 2009 · 8 claims · 7 setups

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SNPs within CpG islands are associated with allele-specific DNA methylation differences between alleles.

leukocytes leukocyte hek293 bisulfite methylation-sensitive cdna
The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation.

PMID 39549198 · PMC11979089 · GeroScience · 2025 · 9 claims · 2 setups

Has reproduction · 54

The Multi-State Epigenetic Pacemaker (MSEPM) can accurately model multiple methylation-associated factors (e.g., age, sex, cell-type) simultaneously.

blood simulated methylation simulation
DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

PMID 15550986 · PMC529316 · PLoS biology · 2004 · 8 claims · 3 setups

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The human MHC methylation profile is strongly bimodal, with the vast majority of analysed regions being either hypo- (≤30%) or hypermethylated (≥70%)

mhc subset heterogeneously bisulphite maldi-ms sub-cloning
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

Has reproduction

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

nasal aggregated severe differentially genome methylation differential
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

Has reproduction · 80

BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr
Methods for genome-wide analysis of DNA methylation in intestinal tumors.

PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

cd19+ lung gpx1 tumor mira medip goldengate
pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS).

PMID 31035919 · PMC6489300 · BMC bioinformatics · 2019 · 7 claims · 8 setups

Has reproduction · 88

pwrEWAS is a user-friendly tool (R package and Shiny web interface) for comprehensive power estimation in two-group EWAS using Illumina HumanMethylation BeadChip technology.

saliva blood cord-blood pbmc illumina simulation
Pleiotropic effects of MORC2 derive from its epigenetic signature.

PMID 40302207 · PMC12782172 · Brain : a journal of neurology · 2026 · 8 claims · 8 setups

Has reproduction

A MORC2-specific DNA methylation episignature exists that is universal across all MORC2-associated phenotypes and conserved across blood and fibroblast tissue

blood fibroblasts fibroblast patient-derived methylation svm phenotype-specific
Epigenetics and phenotypic variation in mammals.

PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

mammalian mhc chromosomes embryonic methylation high-throughput chip
Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups

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KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse

embryonic fetal monochromosomal fibroblasts allele-specific rt-pcr chromatin
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

Has reproduction · 73

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.

blood tcga gse40279 most illumina supervised unsupervised
Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.

PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 6 claims · 6 setups

Has reproduction · 62

RHEB promoter hypermethylation is a PCNSL-specific biomarker distinguishing PCNSL from other CNS diseases.

datasets cns tcga gdc 450k rrbs roc
Inactivation of O6-methylguanine-DNA methyltransferase by promoter CpG island hypermethylation in gastric cancers.

PMID 12085181 · PMC2375420 · British journal of cancer · 2002 · 6 claims · 8 setups

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Loss of MGMT expression in gastric carcinomas frequently results from promoter CpG island hypermethylation.

gastric consecutive snu-620 methylation-specific immunohistochemistry western
Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

PMID 15860770 · PMC1087791 · Nucleic acids research · 2005 · 8 claims · 4 setups

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A Geniom One-synthesized oligonucleotide microarray can determine the methylation status of individual CpG dinucleotides in parallel, combining high throughput with single-base resolution

hct116 p16 genomic methylation-specific combined oligonucleotide
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

PMID 19835597 · PMC2770485 · Molecular cancer · 2009 · 8 claims · 8 setups

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MLL-mutant (MLL mu) AML cell lines show significantly lower TSG promoter methylation than MLL wild-type (MLL wt) AML cell lines

acute mll lines bone ms-mlpa hhai methylation-specific
Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

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Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

peripheral mhc2ta pcr sanger bisulfite cpg
Genome-scale approaches to the epigenetics of common human disease.

PMID 19844740 · PMC3107986 · Virchows Archiv : an international journal of pathology · 2010 · 7 claims · 8 setups

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DNA methylation is a stable, mitotically heritable epigenetic mark faithfully propagated by DNMT1 acting on hemimethylated DNA during replication

autopsy colorectal colon genomic charm quantitative bisulfite
CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

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RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite

Experiments

High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer.

Non-imprinted allele-specific DNA methylation on human autosomes.

The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation.

DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

Methods for genome-wide analysis of DNA methylation in intestinal tumors.

pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS).

Pleiotropic effects of MORC2 derive from its epigenetic signature.

Epigenetics and phenotypic variation in mammals.

Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use.

Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.

Inactivation of O6-methylguanine-DNA methyltransferase by promoter CpG island hypermethylation in gastric cancers.

Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

Genome-scale approaches to the epigenetics of common human disease.

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.