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).

• Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

  PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

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  DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

  cd19+ leukemia raji jurkat quantitative cobra chromatin

• Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions.

  PMID 15958788 · PMC1150895 · Nucleic acids research · 2005 · 6 claims · 4 setups

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  SNaPshot primers with mismatches to upstream bisulfite-induced C/T or G/A polymorphisms produce a position-dependent biasing effect of up to 70%, decreasing as the mismatch moves farther upstream of the target cytosine

  comt synthetic genomic snapshot

• 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

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.

  PMID 30332484 · PMC6192621 · PloS one · 2018 · 7 claims · 8 setups

  Has reproduction · 63

  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.

  k562 hek293t motif luciferase bidirectional

• Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

  PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

  pediatric tumor eight desmoplastic aprimes bisulfite quantitative

• Optical mapping discerns genome wide DNA methylation profiles.

  PMID 18667073 · PMC2516518 · BMC molecular biology · 2008 · 6 claims · 3 setups

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  Methylated restriction sites can be identified in optical maps as cleavage sites that are absent relative to the in silico (sequence-based) restriction map, since most restriction enzymes fail to cut methylated cognate sequences.

  escherichia embryonic optical

• 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

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  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

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• 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

• MMASS: an optimized array-based method for assessing CpG island methylation.

  PMID 17041235 · PMC1635254 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  MMASS-v2 (optimized AciI/HinP1I/HpyCH4IV/HpaII enzyme combination with McrBC digestion) offers improved sensitivity and statistical power for microarray-based CpG island methylation detection compared to MMASS-v1, MMASS-sub and the Nouzova method

  hct116 sssi-methylated hcgi12k methylation spike-in cobra

• MSH6 missense mutations are often associated with no or low cancer susceptibility.

  PMID 15354210 · PMC2409912 · British journal of cancer · 2004 · 7 claims · 8 setups

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  Most MSH6 missense changes found in MSI-positive tumours are likely clinically innocent or of low cancer-susceptibility significance

  microdissected blood individuals paraffin-embedded microsatellite exon sscp

• CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.

  PMID 18725978 · PMC2518116 · PloS one · 2008 · 7 claims · 6 setups

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  TP53 mutations, especially those affecting the L2/L3 DNA-binding domains, are associated with resistance (progressive disease) to epirubicin therapy

  snap-frozen tumor u-2-os patients pcr bisulphite loss

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• 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

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

  chromosome genomic comparative phylohmmcons conserved