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).

• Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.

  PMID 41736854 · PMC12927100 · iScience · 2026 · 7 claims · 6 setups

  Has reproduction · 70

  Early-stage (prodromal) aSyn pathology in M83+/+ mouse brainstem is associated with upregulation of ATP/energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)

  sagittal st-derived spatial immunofluorescence cell-cell

• An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.

  PMID 41577803 · PMC12920623 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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  Inflammatory CAFs (iCAFs) predominate in LUAD, whereas myofibroblastic CAFs (mCAFs) predominate in LUSC

  nsclc epithelial macrophage caf scrna-seq copy gene-set

• A pan-cancer single-cell transcriptomic atlas of human bone metastases.

  PMID 41619722 · PMC12923970 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Constructed a pan-cancer single-cell transcriptomic atlas of 62 human bone metastases (predominantly spinal) across 13 primary cancer types, with paired primary tumor and normal bone marrow samples.

  bone paired plasmacytoma malignant scrna-seq ihc infercnv

• Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

  PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

  aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr

• A spatially resolved human glioblastoma atlas reveals distinct cellular and molecular patterns of anatomical niches.

  PMID 41714633 · PMC13031279 · Nature communications · 2026 · 8 claims · 6 setups

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  GBM exhibits distinct cellular and molecular patterns organized by anatomical niche, with malignant, vascular, and immune compartments showing region-specific spatial associations

  gbm glioma single-cell scrna-seq cite-seq spatial

• Decoding the Mechanisms of Hepatocellular Carcinoma Cancer Stem Cells and Identifying Potential Therapeutic Strategies Based on Single-cell Omics.

  PMID 41771574 · PMC12951371 · Cancer genomics & proteomics · 2026 · 7 claims · 8 setups

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  Malignant cells from HCC tumors resolve into six transcriptionally distinct subpopulations, including a progenitor-like CSC subset expressing EPCAM, SOX9, and SOX4

  malignant tumor csc six single-cell spatial copy

• Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations.

  PMID 41840060 · PMC13125306 · Scientific reports · 2026 · 8 claims · 7 setups

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  IDC exhibits significantly higher CNV burden than DCIS, supporting progressive genomic instability during tumor evolution

  her2-positive epithelial malignant tcga-brca single-cell spatial infercnv

• Single-cell spatial transcriptomics reveals tumor microenvironment heterogeneity in primary and lymph node-metastatic small cell lung cancer.

  PMID 41916294 · PMC13130650 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Three malignant subclusters (C5, C6, C9) are enriched in LNM tumors and display distinct metabolic and angiogenic programs alongside spatial immune exclusion

  pt-lnm spatial single-cell multi-organ single-cell multiplex h&e

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

  PMID 42063567 · PMC13127482 · iScience · 2026 · 8 claims · 8 setups

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  LUSC arising within UIP originates from AT2-derived metaplastic basal cells

  fresh-frozen same scrna-seq paired single-cell copy ligand-receptor

• Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice.

  PMID 40629142 · PMC12321585 · Nature neuroscience · 2025 · 8 claims · 8 setups

  Has reproduction · 82

  Ganglionic eminence (ventral) progenitors maintain stable differentiation competence throughout neurogenesis, generating a consistent set of postmitotic precursor states at all stages, unlike dorsal cortical progenitors whose differentiation competence changes gradually.

  dlx5 progenitors sections cortical scrna-seq trackerseq flashtag

• Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

  PMID 41542331 · PMC12802566 · Health science reports · 2026 · 7 claims · 8 setups

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  BPC differentiation is significantly altered in UC, driven by a FABP1-led functional gene matrix

  colorectal colon patients bulk single-cell spatial bulk

• Endothelial PDGF Signaling Dysregulation Impairs Testicular Interstitial Homeostasis in Diabetes.

  PMID 41643060 · PMC13073339 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 7 setups

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  Testicular endothelial cells (TECs) function as a central signaling hub coordinating intercellular communication within the human testicular interstitium

  testicular testis leydig diabetic single-cell integrative cell-cell

• Single-cell and spatial transcriptomics analyses reveal tumor microenvironment-driven proliferation of NF2-associated vestibular schwannomas.

  PMID 41957607 · PMC13200446 · Journal of neuroinflammation · 2026 · 8 claims · 7 setups

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  NF2-VS tumors comprise 12 major cell lineages with distinct TME composition between Gardner and Wishart phenotypes

  vestibular fresh nf2-vs fibroblast scrna-seq spatial multiplex

• Dissecting origin factors of lymph node metastasis in non-small cell lung cancer via multimodal omics.

  PMID 41975179 · PMC13250061 · Nature communications · 2026 · 8 claims · 8 setups

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  Epithelial cells in mLNs and matched mLN+ primary tumors (mLN+PTs) show enhanced cancer stemness (higher CytoTRACE scores) compared to mLN-negative and normal samples.

  patient-matched mln epithelial tcga-luad scrna-seq spatial cytotrace

• Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

  PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

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  BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

  gastrulating gastrula gold-standard embryo single-cell computational promoter

• Niacin promotes motor function recovery after spinal cord injury via Hcar2-dependent microglia immunometabolic regulation.

  PMID 42068080 · PMC13135113 · Clinical and translational medicine · 2026 · 8 claims · 8 setups

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  Hcar2 is a microglia-enriched gene whose spinal cord expression is upregulated after SCI, peaking at 7 days post-injury

  spinal c57bl bv2 single-cell bulk sci

• DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.

  PMID 41761000 · PMC13043845 · Discover oncology · 2026 · 8 claims · 8 setups

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  Neuroactive ligand–receptor signaling is among the most significantly upregulated pathways in LUAD relative to normal lung tissue.

  tcga-luad tcga luad dendritic-cell bulk survival pan-cancer

• FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis.

  PMID 41839892 · PMC13201544 · Nature communications · 2026 · 8 claims · 6 setups

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  FineST, a bimodal contrastive learning model integrating histology (Virchow2 ViT features) and spatial gene expression, enables nuclei-resolved high-resolution RNA imputation.

  colorectal crc breast he-stained spatial type ccc