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).

• Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

  PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

  inhbb cloned same fresh-frozen rnase masscleave clonal

• Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.

  PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups

  Has reproduction · 99

  Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.

  coli lymphoblastoid na12878 mixture nanopore cas9-targeted whole-genome

• Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

  PMID 18413340 · PMC2425484 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  CpG-rich regions (CpG islands) show low and similar methylation levels across individuals, but the sequential order of the few methylated CpGs among the many unmethylated ones varies randomly between individuals.

  cd4+ computational hep direct simulation epigraph

• 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

• 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

• 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

• 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

• Heterogeneous genomic molecular clocks in primates.

  PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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  Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

  baboon chimpanzee same human-chimpanzee relative phylogenetic four-species

• Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.

  PMID 17855401 · PMC2094075 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  LDSS analysis identifies octamer sequences with localized distribution profiles as promoter constituents, classifiable into groups (REG, TATA, Inr, Kozak, CpG, Y Patch)

  arabidopsis rice promoter cross-species ldss sequence distribution

• 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 gene guessing game.

  PMID 11025532 · PMC2448377 · Yeast (Chichester, England) · 2000 · 8 claims · 6 setups

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  Published methods for estimating human gene number diverge widely, from ~30,000 to over 140,000 genes.

  genomic ests tetraodon genome cpg est comparative

• DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia.

  PMID 19102774 · PMC2630979 · BMC medical genetics · 2008 · 8 claims · 6 setups

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  Variation in SYN III distal CpG island methylation is not related to schizophrenia in the population sample or in a monozygotic twin pair discordant for schizophrenia

  brain blood non-human semi-quantitative sodium bisulfite

• MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

  PMID 16381984 · PMC1347458 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  MPromDb is a novel database integrating experimentally supported gene promoters, TSS annotation, cis-regulatory elements, CpG islands, and ChIP-chip data with an integrated visualization interface.

  chip-chip sequence genbank

• Human epigenome project--up and running.

  PMID 14691553 · PMC300691 · PLoS biology · 2003 · 7 claims · 4 setups

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  Epigenetic modifications (e.g., DNA methylation) rather than DNA sequence differences explain phenotypic differences between genetically identical individuals, such as monozygotic twins or inbred mice.

  expressed bat8 genetically methylation genome-wide phenotypic

• Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

  PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

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  QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

  paired colorectal genome normal quma auma bioinformatic

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

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

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  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

• Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas.

  PMID 16224153 · PMC2779276 · Journal of Korean medical science · 2005 · 7 claims · 4 setups

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  High-level-loss (LOH-H) tumors show a tendency toward unmethylation in Maspin, CAGE, MAGE-A2, and RABGEF1 genes

  microdissected same bisulfite-modified pcr microsatellite methylation-specific bisulfite

• Patterns and rates of intron divergence between humans and chimpanzees.

  PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups

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  Intron divergence (Ki) is strongly positively correlated with intron length

  orthologous genome whole-genome cpg recombination

• Periodicity of SNP distribution around transcription start sites.

  PMID 16579865 · PMC1448210 · BMC genomics · 2006 · 8 claims · 6 setups

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  SNP density around TSS shows a 146-nucleotide periodicity

  genome human-chimpanzee tss promoter snp sequence cpg

• 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