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).

• Genetic and epigenetic contributions to human nutrition and health: managing genome-diet interactions.

  PMID 18755320 · PMC5421377 · Journal of the American Dietetic Association · 2008 · 8 claims · 7 setups

  Full-text index only

  Folate-mediated one-carbon metabolism is a conduit linking the cellular nutrient environment to genome regulation via nucleotide biosynthesis for DNA synthesis and SAM biosynthesis for genome methylation.

  yellow premenopausal men humans dietary mthfr plasma

• Coexistence of two different pseudohypoparathyroidism subtypes (Ia and Ib) in the same kindred with independent Gs{alpha} coding mutations and GNAS imprinting defects.

  PMID 19858129 · PMC3030964 · Journal of medical genetics · 2010 · 7 claims · 5 setups

  Full-text index only

  Two unrelated PHP-I families each include at least one patient with a Gsα coding mutation (PHP-Ia) and another with GNAS imprinting defects (PHP-Ib)

  genomic erythrocyte gnas sanger methylation-specific microsatellite

• An integrative genomic and epigenomic approach for the study of transcriptional regulation.

  PMID 18365023 · PMC2266992 · PloS one · 2008 · 8 claims · 7 setups

  Full-text index only

  Integrative analysis combining gene expression, DNA methylation, and H3K9 acetylation data reveals hundreds of additional differentially expressed genes missed by gene expression arrays alone

  aml computational help chip-chip gene

• Epigenetics and phenotypic variation in mammals.

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

  Full-text index only

  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

• 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

• Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

  PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

  Full-text index only

  Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

  chromosome genomic pbmc multi-species phylogenetic bisulphite

• The stem cell population of the human colon crypt: analysis via methylation patterns.

  PMID 17335343 · PMC1808490 · PLoS computational biology · 2007 · 8 claims · 3 setups

  Full-text index only

  A coalescent-based, full probabilistic model with MCMC Bayesian inference provides a more powerful alternative to prior forward-simulation approaches for analyzing methylation pattern data from crypts.

  colon computational simulated bisulfite coalescent posterior

• The role of X-chromosome inactivation in female predisposition to autoimmunity.

  PMID 11056674 · PMC17816 · Arthritis research · 2000 · 6 claims · 2 setups

  Full-text index only

  Skewed X-chromosome inactivation in the thymus could lead to inadequate thymic deletion of T cells reactive to X-linked polymorphic self-antigens, predisposing to autoimmunity

  peripheral fluorescent pcr

• 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

  Full-text index only

  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

• Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

  PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  KYNU expression is decreased in melanoma despite a high KYNU mutation rate in the TCGA database

  tcga-skcm melanoma keratinocytes differential copy methylation

• Widely variable endogenous retroviral methylation levels in human placenta.

  PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups

  Full-text index only

  Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters

  term placenta genome bisulfite rt-pcr genome-wide

• MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

  PMID 17480217 · PMC1868705 · BMC medical genetics · 2007 · 8 claims · 7 setups

  Full-text index only

  The MRX87 disease locus maps to the Xp22-p21 interval, a known hot spot region for mental handicap

  peripheral genomic pcr leukocytes two-point direct pcr

• 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

• Adverse prognosis of epigenetic inactivation in RUNX3 gene at 1p36 in human pancreatic cancer.

  PMID 18475302 · PMC2391125 · British journal of cancer · 2008 · 7 claims · 5 setups

  Full-text index only

  RUNX3 promoter hypermethylation is frequent in primary pancreatic cancer tissue

  pancreatic microsatellite methylation-specific bisulphite

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 6 claims · 7 setups

  Has reproduction · 91

  A hybrid de novo assembly combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X) produced the YO draft genome Ogye_1.1 with contig and scaffold NG50 of 362.3 Kbp and 16.8 Mbp.

  yeonsan tissues ogye_1.1 locus whole-genome sequencing reduced

• MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.

  PMID 19906696 · PMC2811030 · Nucleic acids research · 2010 · 6 claims · 4 setups

  Full-text index only

  MiGS combines MBD2 MBD-domain precipitation of methylated DNA with massively parallel sequencing to enable unbiased, high-throughput genome-wide DNA methylation profiling

  hct116 migs mbd-isolated bisulfite gene

• A novel mutation in FRMD7 causing X-linked idiopathic congenital nystagmus in a large family.

  PMID 18246032 · PMC2267738 · Molecular vision · 2008 · 8 claims · 6 setups

  Full-text index only

  A novel c.812G>T transversion in exon 9 of FRMD7, causing p.C271F, is the causative mutation for XLICN in this family

  affected family blood frmd7 microsatellite direct denaturing

• Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

  PMID 27843499 · PMC5105311 · Mobile DNA · 2016 · 6 claims · 7 setups

  Has reproduction · 67

  Canonical (endonuclease-dependent, TPRT-driven) L1 retrotransposition is absent or negligible in GBM tumours and cultured GBM cell lines

  brain tumour gbm retrotransposon empty qrt-pcr

• Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

  PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

  chromosome genomic comparative phylohmmcons conserved

• SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

  PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

  Full-text index only

  SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

  single hcc2218 nsclc array gene multi-omics