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).

• H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity.

  PMID 40764058 · PMC12487818 · Genome research · 2025 · 8 claims · 8 setups

  Has reproduction · 55

  H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding

  imefs early ctcf h3k9me3 h3k9me2

• CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.

  PMID 17981843 · PMC2238977 · Nucleic acids research · 2008 · 7 claims · 8 setups

  Full-text index only

  CTCF is the only identified trans-acting factor in vertebrates that confers enhancer-blocking insulator activity

  ohlsson ren zhao tissues chip-chip massive motif

• Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

  PMID 18684996 · PMC2532738 · Nucleic acids research · 2008 · 8 claims · 7 setups

  Full-text index only

  SISSRs identifies binding sites from ChIP-Seq short reads with much higher resolution than the standard region-clustering approach

  cd4+ jurkat hela computational chip-seq novo motif

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining

• 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