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).

• An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage.

  PMID 41618446 · PMC12934089 · Genome biology · 2026 · 8 claims · 6 setups

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  3D genome structure and chromatin accessibility change dramatically as early as 4 h after all-trans-retinoic acid (ATRA) treatment, preceding major transcriptional changes.

  hl-60 ocean-c atac-seq rna-seq

• FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

  PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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  FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

  prostate targeted single-nucleus scatac-seq

• MerTK-triggered TGFβ1 autocrine signal regulates microglial response to neurodegeneration.

  PMID 41634038 · PMC12976283 · Nature communications · 2026 · 8 claims · 8 setups

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  Microglial response to pathological axonal degeneration (optic nerve injury) depends on the phagocytic receptor MerTK

  optic facs-sorted microglia co-immunostaining qpcr bulk

• ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.

  PMID 41639613 · PMC12973882 · BMC bioinformatics · 2026 · 8 claims · 8 setups

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  ChromAcS is a comprehensive open-source, GUI-based ATAC-seq analysis pipeline supporting multi-species genomes with real-time progress monitoring and modular re-execution.

  pc9 paired-end sorted atac-seq quality read

• Multi-omics analysis of somatic mutants reveals TCP7 allelically regulates multiple carotenogenic genes in citrus.

  PMID 41664139 · PMC12888363 · Molecular horticulture · 2026 · 7 claims · 7 setups

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  Red-fleshed and orange-fleshed Guanxi pomelo arose from two independent somatic mutation events from the same white-fleshed wild type

  pomelo wild-type rt-qpcr carotenoid genome

• M(5)C-driven stabilization of SERPINB5 promotes cervical cancer progression and chemotherapy resistance.

  PMID 41673397 · PMC12921336 · Cell death & disease · 2026 · 8 claims · 8 setups

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  RNA m5C levels are globally and consistently elevated in cervical tumors compared to normal cervical tissue

  cervical hela nsun2 bisulfite bulk spatial

• Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.

  PMID 41674383 · PMC12895067 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  HNRNPU forms extensive protein networks including an association with the mammalian SWI/SNF chromatin-remodeling complex

  ipsc-derived computational neocortical ip-ms formaldehyde alphapulldown expression-weighted

• Excitatory GABA receptors shape locomotor circuit organization in C. elegans.

  PMID 41703147 · PMC13003095 · Scientific reports · 2026 · 8 claims · 5 setups

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  lgc genes are broadly and preferentially enriched in C. elegans locomotion motor neurons compared to other neuron types/subgroups

  elegans cys-loop single-cell ucell multi-species

• 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

• RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis.

  PMID 41746718 · PMC13078889 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  LARP6 is upregulated in activated hepatic stellate cells (A1/A2 subclusters) in human MASH and MetALD livers

  hepatic liver recombinant activated eclip ribosome single-nucleus

• Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes.

  PMID 41782826 · PMC12955150 · iScience · 2026 · 8 claims · 6 setups

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  Tet2-deficient NOD mice transplanted with WT bone marrow show fewer islet-infiltrating lymphocytes beginning 8–10 weeks post-transplant, primarily among CD4+ T cells

  islets islet islet-infiltrating cadaveric flow single-cell single-nucleus

• Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci.

  PMID 41807385 · PMC12979833 · Nature communications · 2026 · 8 claims · 8 setups

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  Integration of CAD GWAS summary statistics with epigenetic data from 45 cell types identifies 1580 candidate CAD genes

  cad-associated disease-relevant types cad variant epigenetic tf-snv

• Adhesion-Related Macrophages Regulate Metabolic Homeostasis Through CAV-1 Dependency.

  PMID 41817010 · PMC13159151 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  Adhesion-related macrophages (ARMs) are a distinct macrophage subpopulation that adheres directly to adipocytes and can be isolated using a novel vortex/bead-based method

  ewat facs-sorted arms sort-purified flow bulk atac-seq

• Single-cell epigenomics uncovers heterochromatin instability and transcription factor dysfunction during mouse brain aging.

  PMID 41824460 · PMC13189690 · Cell reports · 2026 · 8 claims · 6 setups

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  Aging causes widespread, concordant changes in chromatin accessibility and gene expression across neuronal and glial cell types in the mouse brain

  brain snatac-seq single-nucleus merfish

• EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

  PMID 41832145 · PMC13133354 · Nature communications · 2026 · 8 claims · 7 setups

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  EPInformer outperforms existing gene expression prediction models (Xpresso, CREaTor, Seq-GraphReg, Enformer, Borzoi) in rigorous 12-fold cross-chromosome validation for both RNA-seq and CAGE expression prediction

  k562 lines likely cell-type-specific rna-seq cage abc

• Stimulation to secrete insulin induces pancreatic β-cell dysfunction through Tfe3 activation.

  PMID 41940345 · PMC13049674 · iScience · 2026 · 8 claims · 8 setups

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  Continuous glucose supplementation in mice induces Tfe3 nuclear accumulation in islet β-cells, associated with Mafa downregulation and impaired glucose tolerance

  c57bl pancreas min6 intraperitoneal immunofluorescence insulin

• Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.

  PMID 41946881 · PMC13057473 · Communications biology · 2026 · 8 claims · 7 setups

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  Bivalent domains have higher GC content and stronger evolutionary conservation than monovalent regions

  embryonic mesc random bivalent chip-seq rna-seq k-mer-based

• 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

• Cross-species prediction reveals chromatin regions with increased accessibility in humans.

  PMID 41984952 · PMC13082337 · Science advances · 2026 · 8 claims · 8 setups

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  CNNs trained exclusively on human ATAC-seq data achieve cross-species prediction performance in chimpanzees and macaques comparable to species-specific models

  lymphoblastoid prefrontal six chimpanzee bulk single-cell cnn

• Single-cell epigenetic and transcriptomic states across the continuum of monoclonal B cell lymphocytosis to chronic lymphocytic leukemia.

  PMID 41987205 · PMC13192028 · Genome biology · 2026 · 8 claims · 6 setups

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  The HC-MBL to CLL transition shows subclonal, epigenetic and transcriptomic stability, consistent with a continuous disease spectrum rather than distinct evolutionary phases.

  cd19+ lc-mbl single scrna-seq mtscatac-seq asap-seq