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).

• TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes.

  PMID 35580127 · PMC9159589 · PLoS genetics · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Pigmentation genes are only expressed in mitfa-expressing zebrafish melanocyte-lineage cells that also express tfap2 paralogs

  gfp+ sk-mel-28 tfap2a single-cell crispr atac-seq

• CTCF's loop-independent functions prevail over chromatin looping in the acute degradation system.

  PMID 41191909 · PMC13107559 · Protein & cell · 2026 · 8 claims · 8 setups

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  CTCF regulates Ppa2 and Zbtb39 expression through mechanisms independent of chromatin looping

  ctcf-aid mescs rna-seq chip-seq western

• Cellular insights into transposable elements in Alzheimer's disease.

  PMID 41573740 · PMC12819740 · Frontiers in molecular biosciences · 2025 · 8 claims · 5 setups

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  508 TE loci are differentially expressed in AD brain, with the large majority (84.3%) upregulated, indicating widespread TE activation

  postmortem brain genome genes single-nucleus atac-seq pseudobulk

• Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.

  PMID 41365655 · PMC12758391 · Genome research · 2026 · 8 claims · 3 setups

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  A factor-agnostic MNase-seq chromatin occupancy profiling (COP) approach can simultaneously capture genome-wide TF and nucleosome occupancy at near-nucleotide resolution from a single assay

  saccharomyces cerevisiae mnase-seq gene

• Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments.

  PMID 18765474 · PMC2577354 · Nucleic acids research · 2008 · 6 claims · 6 setups

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  Extensive sonication reduces crosslinked chromatin to an average fragment size of ~200 bp (range 75–300 bp) and fragmentation is largely random with respect to genomic region and nucleosome position.

  cerevisiae hela chip-qpcr nucleosome gel

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman

• Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders.

  PMID 41653922 · PMC13034722 · Molecular cell · 2026 · 8 claims · 8 setups

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  Heterozygous de novo missense mutations in RING1 and RNF2 are found in individuals with neurodevelopmental/intellectual disability phenotypes

  cohorts prc1 ring1a elegans variant structural western

• Engineered apoptotic nucleases for chromatin research.

  PMID 17626049 · PMC1935020 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Inserting TEVP cleavage sites immediately downstream of the two caspase-3 sites in DFF45 (I1I2 mutant) makes DFF40 nuclease activity exclusively dependent on TEVP cleavage (DFF-T)

  recombinant cerevisiae coli western plasmid serial

• Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites.

  PMID 41778583 · PMC12959880 · eLife · 2026 · 8 claims · 8 setups

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  H3K115ac is enriched at the TSS of active CpG island (CGI) promoters, far more than non-CGI promoters

  embryonic mescs synthetic mesc chip-seq atac-seq dot

• Predicting enhancers in mammalian genomes using supervised hidden Markov models.

  PMID 30917778 · PMC6437899 · BMC bioinformatics · 2019 · 8 claims · 8 setups

  Has reproduction · 70

  eHMM predicts enhancers with high precision and recall comparable to state-of-the-art methods and consistently outperforms them in accuracy and resolution

  esc atac-seq chip-seq cage

• Transcription dynamics.

  PMID 19782025 · PMC6326382 · Molecular cell · 2009 · 8 claims · 8 setups

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  Transcription factors locate their sparse specific binding sites via a 3D scanning mechanism combining rapid nuclear diffusion with frequent, very transient (seconds-scale) nonspecific chromatin interactions.

  living linker lac glucocorticoid frap single-molecule nucleosome

• TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

  PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

  Has reproduction · 80

  TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

  imr90 hct116 chip-seq rna-seq atac-seq

• An MNase-ChIP-Seq Protocol to Profile Histone Modifications at a DNA Break in Yeast.

  PMID 41874159 · PMC13010634 · Methods and protocols · 2026 · 6 claims · 5 setups

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  MNase-ChIP-seq, combining MNase-based chromatin fragmentation with ChIP and NGS, is a robust protocol to map histone PTMs and their genome-wide distribution after induction of a single HO-generated DSB in yeast

  cerevisiae extracted crosslinked rt-qpcr qpcr-based mnase-chip-seq

• miRGen 2.0: a database of microRNA genomic information and regulation.

  PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

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  miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

  lung organ malme embryonic polii small nucleosome

• APC coordinates GSK3 phosphorylation of SETD8 to suppress colorectal cancer.

  PMID 41790555 · PMC13123626 · Cell reports · 2026 · 8 claims · 8 setups

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  SETD8 Thr138 (mouse)/Thr140 (human) is a bona fide GSK3 phosphorylation site whose phosphorylation is dependent on APC in vivo and in vitro

  intestinal recombinant apk setd8 phosphoproteomic radioactive western

• Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters.

  PMID 11897022 · PMC139022 · Genome biology · 2002 · 8 claims · 8 setups

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  Trans-splicing generates cell-specific protocadherin mRNAs in human neurons

  individual cancer pre-b saccharomyces reverse-transcriptase karyotypic spectral

• Cell type differences in human cytomegalovirus transcription and epigenetic regulation with insights into major immediate-early enhancer-promoter control.

  PMID 40758707 · PMC12333995 · PLoS pathogens · 2025 · 8 claims · 7 setups

  Has reproduction · 90

  Six viral promoters (UL5, UL72, EP3, UL57-AS, US16-AS, US30-S) are ≥50-fold more active in D-NT2 than in HFF at 96 h post-infection and are classified as viral long promoters.

  d-nt2 hcmv-infected hcmv pro-seq dff-chip promoter