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).

• Probing the cancer genome.

  PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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  Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

  mcf-7 tumor lung oral sanger solexa gistic

• Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

  PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

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  Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

  pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq

• ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.

  PMID 41243977 · PMC12807738 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  ATACdb 2.0 expands data scale, adding mouse chromatin accessibility data and substantially expanding human samples, plus pseudo-bulk ATAC-seq profiles built from scATAC-seq data to increase cell type diversity

  geo scatac-ref bulk scatac-seq h3k27ac

• Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

  PMID 41371963 · PMC12758400 · Genome research · 2026 · 8 claims · 6 setups

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  GSC-like and CySC-like cells isolated from upd tumor testes are transcriptionally comparable to wild-type GSC/early-spermatogonia and CySC clusters, respectively

  upd gsc-like wild-type scrna-seq differential gene

• Transcription and potential functions of a novel XIST isoform in male peripheral glia.

  PMID 41386982 · PMC12863056 · Genome research · 2026 · 8 claims · 8 setups

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  XIST is robustly expressed in male peripheral glia, particularly nonmyelinating Schwann cells, across human heart and skeletal muscle tissue.

  heart skeletal atlas peripheral scrna-seq aggregated scatac-seq

• 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

• The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements.

  PMID 41632506 · PMC12867480 · eLife · 2026 · 8 claims · 8 setups

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  CHD4 acts via a second mechanism beyond nucleosome sliding: actively restricting the residence time of transcription factors on chromatin

  chd4-maid sall1 western flow calibrated

• Epigenetic regulation of serine biosynthesis by PHF8 during neurogenesis.

  PMID 41714361 · PMC13022353 · EMBO reports · 2026 · 8 claims · 8 setups

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  PHF8 is required for neural stem cell (NSC) proliferation in vitro

  developing nscs embryonic single-cell shrna growth

• Isoform-specific single-cell perturb-seq reveals distinct functions of alternative promoters in drug response.

  PMID 41728950 · PMC12926921 · Nucleic acids research · 2026 · 5 claims · 8 setups

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  CRISPR-dCas9-based screens exhibit widespread promoter specificity, with untargeted promoters often showing compensatory upregulation to maintain overall gene expression

  mcf-7 rpe1 mcf-7-dcas9 tissue-wide isoform-specific reanalysis qrt-pcr

• Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila.

  PMID 41735587 · PMC12987734 · Nature genetics · 2026 · 8 claims · 8 setups

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  Pico-C, a low-input Micro-C method, enables high-resolution, temporally resolved 3D genome mapping in early Drosophila embryos using as few as ~60,000 nuclei

  hand-staged early drosophila pico-c chip-seq atac-seq

• PVT1 lincRNA signals an androgen-dependent transcriptional activation program of oncogenes in prostate cancer cells.

  PMID 41792045 · PMC13139993 · International journal of cancer · 2026 · 8 claims · 7 setups

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  PVT1 knockdown significantly reduces LNCaP cell proliferation and increases sensitivity to apoptosis

  lncap tcga-prad rt-qpcr trypan transwell

• Mechanisms of gene regulation by SRCAP and H2A.Z.

  PMID 41792122 · PMC13087030 · Nature communications · 2026 · 8 claims · 8 setups

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  Acute SRCAP degradation causes rapid, genome-wide replacement of H2A.Z by canonical H2A, with turnover fastest at active promoters/enhancers and slower at bivalent loci

  syat cut&run live h2a.z

• Genetic alternative splicing regulation mapping of cartilage and synovium reveals tissue-specific mechanisms of joint-related traits.

  PMID 41820402 · PMC13121699 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a splicing quantitative trait loci (sQTL) resource for human cartilage and synovium from over 200 donors

  degenerated synovium matched paired bulk genotyping differential

• Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity.

  PMID 41842971 · PMC13132380 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  PRC2i/EZH2i alone or combined with AR inhibitors induce diverse cell state programs (CSPs) that increase tumor cell invasion, metastasis, and drug resistance despite only modest suppression of tumor growth.

  lncap pca pdx clinical viability tumor ic50

• Evolution of a distinct chromatin regulatory landscape in brown algae.

  PMID 41896322 · PMC13076208 · Nature ecology & evolution · 2026 · 8 claims · 6 setups

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  Brown algae lost DNA methyltransferases (DNMT1, DNMT3, DNMT5) early in their evolution, retaining only DNMT2/TRDMT homologues

  ectocarpus histone same computational mass western chip-seq

• An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.

  PMID 41922356 · PMC13212934 · Nature communications · 2026 · 8 claims · 7 setups

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  BioSeq2Seq is a transformer-based deep learning framework that predicts genome-wide transcriptional regulatory profiles at 128-bp resolution by jointly using RO-seq data and DNA sequence as tri-modal input

  k562 gm12878 imr-90 ro-seq chip-seq functional

• Developmental stage dominates cell-type identity and reveals a chromatin regulatory function for Rad50 in Drosophila.

  PMID 41978263 · PMC13076223 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Developmental stage is a stronger determinant of transcriptional identity than cell type across Drosophila neurons, glia, and hemocytes

  neurons cns e16 salivary bulk atac-seq western

• BCG-trained macrophages promote pan-anti-tumor activity through epigenetic rewiring of NOX2-ROS axis.

  PMID 42032669 · PMC13261971 · Journal of experimental & clinical cancer research : CR · 2026 · 7 claims · 8 setups

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  BCG training induces pan-anti-tumor activity across multiple mouse tumor models, mediated predominantly by tumor-associated macrophages (TAMs)

  llc tumor-infiltrating macrophage raw264.7 tumor flow antibody-mediated

• Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.

  PMID 33086062 · PMC7649750 · Cell reports · 2020 · 8 claims · 8 setups

  Has reproduction · 59

  KMT2D is a potent tumor suppressor in melanoma

  hmel-brafv600e tyr-creert2 tma kmt2d pooled xenograft genetically

• An Erg-driven transcriptional program controls B cell lymphopoiesis.

  PMID 32541654 · PMC7296042 · Nature communications · 2020 · 7 claims · 8 setups

  Has reproduction · 81

  Erg is essential for early B lymphoid differentiation

  erg b220+ prob wild-type lacz rna-seq flow