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).

• Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

  PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

  Has reproduction · 90

  MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

  pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent

• Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity.

  PMID 41950003 · PMC13244359 · Cell reports · 2026 · 8 claims · 7 setups

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  Multi-omics factor analysis (MOFA) integrating seven omics views from 1,358 ROS/MAP participants identifies cross-omics biological factors relating to AD phenotypes.

  dorsolateral brain postmortem cortex h3k9ac bulk proteomics

• Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.

  PMID 41484656 · PMC12857045 · Genome biology · 2026 · 8 claims · 8 setups

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  pRIC-seq, an adaptation of RIC-seq for plants, enables genome-wide mapping of RNA-RNA spatial interactions in diploid and tetraploid cotton

  diploid tetraploid cotton nicotiana pric-seq gro-cap chip-seq

• From linear genome sequence to three-dimensional organization of the cell nucleus.

  PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

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  Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

  saccharomyces mitotic nucleoplasm hela chromosome translocation stretched

• Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes.

  PMID 41526351 · PMC12796357 · Nature communications · 2026 · 8 claims · 8 setups

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  Cardiomyocyte (CM)-specific Hi-C data detect substantially more and stronger promoter-interacting domains (PIDs) for CM marker genes than bulk cardiac tissue Hi-C data

  non-failing cardiac nf-lv-cm biological hi-c fluorescence-activated chip-seq

• Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data.

  PMID 41633996 · PMC12976324 · Nature communications · 2026 · 8 claims · 8 setups

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  ICE and KR matrix balancing normalization methods over-correct and attenuate low-frequency enhancer-promoter loop signals despite preserving structural (CTCF-mediated) loops

  gm12878 embryonic mescs hi-c chip-seq chia-pet

• Cis-Regulation of the CFTR Gene in Pancreatic Cells.

  PMID 40332394 · PMC12027686 · International journal of molecular sciences · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  Multiple active CREs exist upstream and downstream of the CFTR gene in pancreatic (Capan-1) cells, identified via ATAC-seq, CUT&RUN-seq (H3K27ac), 4C-seq, and the ABC model

  capan-1 caco-2 hepg2 atac-seq cut&run-seq 4c-seq

• Sequencing the regulatory genome.

  PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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  Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

  interphase nine beta-globin drosophila nuclear digital chip

• ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae.

  PMID 40364978 · PMC12067309 · Bio-protocol · 2025 · 8 claims · 6 setups

  Has reproduction · 100

  Spike-in normalization, though semiquantitative, often fails to reliably support comparisons within and between ChIP-seq samples.

  cerevisiae pombe sequenced concatenated chip-seq fastq read

• Toward stem cell systems biology: from molecules to networks and landscapes.

  PMID 19329576 · PMC2738746 · Cold Spring Harbor symposia on quantitative biology · 2008 · 7 claims · 6 setups

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  Stem-cell-fate specification is an extremely complex process regulated by multiple mutually interacting molecular mechanisms with numerous regulatory feedback loops.

  stem embryonic promyelocytic genome-wide serial chip-chip

• Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities.

  PMID 18617507 · PMC2577208 · Molecular & cellular proteomics : MCP · 2008 · 8 claims · 8 setups

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  Nuclear Ran GTPase was identified by mass spectrometry as a novel interacting partner of VRK1 and VRK2B

  hek293t recombinant hela gst western co-immunoprecipitation

• Remodeling of XIST regulatory landscape during primate evolution.

  PMID 41544163 · PMC12810636 · Science advances · 2026 · 8 claims · 8 setups

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  XIST regulation has diverged uniquely and rapidly between closely related primates: JPX is a major XIST regulator in human and marmoset ESCs but only a minor regulator in macaque ESCs

  lyon-es1 rna-fish bulk capture

• Exonic enhancers are a widespread class of dual-function regulatory elements.

  PMID 41927541 · PMC13216554 · Nature communications · 2026 · 8 claims · 8 setups

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  Many protein-coding exons possess enhancer activity across species, forming a class of candidate Exonic Enhancers (cEEs)

  coding k-562 cloned garre1 chip-seq dnase histone

• RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions.

  PMID 41951674 · PMC13103356 · Nature communications · 2026 · 8 claims · 8 setups

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  RB colocalizes extensively with cohesin (SMC3) genome-wide, especially at insulators

  htert-rpe1 micro-c fluorescence chip-seq

• CircleBase V2: an eccDNA annotation platform across cancers and species.

  PMID 41273082 · PMC12807720 · Nucleic acids research · 2026 · 8 claims · 7 setups

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  CircleBase V2 provides a 12-fold increase in human eccDNA data, comprising over 3.8 million entries from >300 cell types/tissues

  raw eccdna tissues cancer circle-seq motif gene

• Nanog mediated control of TBX3-GATA6 circuitry in primitive endoderm differentiation of mESCs.

  PMID 41629627 · PMC12979688 · EMBO reports · 2026 · 8 claims · 8 setups

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  NANOG partners with TBX3 and the PRC2 complex to maintain ESC identity by silencing PrE genes through distal enhancers

  rcnβh escs qpcr rna-seq chip-seq

• 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

• STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing sarcoma aggressiveness.

  PMID 41950086 · PMC13079922 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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  STAG2 loss does not globally attenuate EWS-FLI1 activity but reprograms its chromatin binding, redirecting it from short (1-4x) GGAA-repeat sites toward long/multimeric (≥5x) GGAA-repeat microsatellite enhancers

  a673 tc-71 chip-seq immunoblot atac-seq

• The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

  PMID 41625479 · PMC12857760 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

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  Neutrophils in the lung metastatic niche comprise two functionally distinct subsets, Ly6g^high and Ly6g^low, based on Ly6g expression level

  lung cramp cd8+ neutrophils single-cell flow genetic