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).

• Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

  PMID 15686596 · PMC549029 · Molecular cancer · 2005 · 8 claims · 5 setups

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  A chromatin library coupled with experimental validation can productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.

  t-47d agarose chromatin cloning

• 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

• 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

• Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.

  PMID 41547832 · PMC12914055 · Nature communications · 2026 · 8 claims · 8 setups

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  Af-CUT&Tag eliminates dependence on conventional target antibodies by using CRISPR-integrated HiBiT/ALFA-tags recognized by LgBiT/NbALFA-Tn5 fusion proteins

  recombinant sw480 lysates genomic bio-layer chemiluminescent co-immunoprecipitation

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• 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

• Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

  PMID 35260568 · PMC8904849 · Nature communications · 2022 · 7 claims · 8 setups

  Has reproduction · 55

  RBV, a WD40 repeat protein, is required for global microRNA biogenesis in Arabidopsis

  amir-sul col 14-day-old arabidopsis small rna-seq gel

• Protein microarray technology.

  PMID 17126887 · PMC1828913 · Mechanisms of ageing and development · 2007 · 8 claims · 8 setups

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  Protein microarrays enable high-throughput characterization of protein biochemical activities across an entire proteome in a single experiment

  yeast sh2 protein-protein protein-dna chromatin

• Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a.

  PMID 18096052 · PMC2246272 · Genome biology · 2007 · 6 claims · 4 setups

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  Suv39h1 and G9a associate with previously reported methylation states (Suv39h1 with H3K9me3; G9a with H3K9me/me2)

  crude hela-suv39h1 suv39h1 normal propionylation-based double maldi-tof

• 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