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).

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

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

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

  ohlsson ren zhao tissues chip-chip massive motif

• CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

  PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

  Full-text index only

  CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

  cd4+ hela imr90 embryonic chip-seq computational gene

• Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

  PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups

  Has reproduction

  Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types

  types encode chip-seq chromhmm dnase-seq

• 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

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  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

• Segzoo: a turnkey system that summarizes genome annotations.

  PMID 42087325 · PMC13189851 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 4 setups

  Full-text index only

  Segzoo is a turnkey system that automates downloading of reference data and running of analyses to summarize SAGA genome annotations, requiring only a BED-format annotation file as input

  embryonic segway chip-seq segway segtools

• Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

  PMID 40281430 · PMC12032694 · BMC genomics · 2025 · 7 claims · 8 setups

  Full-text index only

  A large repository of nascent run-on RNA-seq samples (DBNascent) was assembled and uniformly processed to identify sites of bidirectional transcription genome-wide.

  bidirectional across high-quality nascent comparative eqtl

• 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

  Transcriptional bursting kinetics is regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 (PRC2) and transcription elongation factors

  cast knock-in mesc mescs single-cell single-molecule 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

• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

  PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 49

  B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

  dlbcl normal same lymphoma help errbs massarray

• Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer.

  PMID 41412800 · PMC12849445 · Genes & development · 2026 · 7 claims · 7 setups

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  H3K9 methylation and the demethylase KDM4C, through association with SWI/SNF, drive proliferation of cells fated to become endocrine-resistant via a nongenomic estrogen-mediated mechanism

  parental t47d esr1 scrna-seq hi-c atac-seq

• 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