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 engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

  PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 88

  SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

  kidney tubuloids immunodeficient tub rt-qpcr western histology

• Single-Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression.

  PMID 34825784 · PMC8787427 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022 · 8 claims · 6 setups

  Has reproduction · 59

  Human NP contains six transcriptionally distinct NPC subpopulations: HT-CLNPs, effector NPCs, homeostatic NPCs, regulatory NPCs, fibroNPCs, and adhesion NPCs

  npcs scrna-seq-derived ht-clnp-i g-mdscs single-cell rt-qpcr immunohistochemistry

• CD14(lo)CD301b(+) macrophages gathering as a proangiogenic marker in adipose tissues.

  PMID 39645040 · PMC11745947 · Journal of lipid research · 2025 · 8 claims · 8 setups

  Has reproduction · 59

  Cd14−/− mice exhibit a leaner body shape and are protected from HFD-induced obesity compared to WT mice

  epididymal adipose cd14low macrophage bulk scrna-seq pseudotime

• YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.

  PMID 41533786 · PMC12802833 · Science advances · 2026 · 8 claims · 8 setups

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  TAZ represses PPARγ-bound target enhancers, evidenced by markedly reduced H3K27ac occupancy, leading to transcriptional repression of adipogenic genes including Pparg2

  c3h10t1 inguinal iwat adipose atac-seq rna-seq immunoblot

• Paneth cell SIRT1 deficiency increases intestinal stress resistance by modulating the gut microbiota.

  PMID 41826553 · PMC13076647 · EMBO reports · 2026 · 8 claims · 8 setups

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  Generated a novel Paneth-cell-specific SIRT1 knockout mouse model (SIRT1 PKO, Sirt1 f/f;Defa6-Cre+)

  small immune facs-sorted ileum single-cell facs qpcr

• Multi-Omics reveals SPP1 + malignant and CXCR4(+) TAM crosstalk predicts immunotherapy response in lung adenocarcinoma.

  PMID 42045760 · PMC13187092 · Discover oncology · 2026 · 8 claims · 8 setups

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  SPP1+ malignant and CXCR4+ TAM crosstalk drives CD8 T cell exhaustion and induces poor immunotherapy response

  luad tcga-luad epithelial a549 single-cell spatial bulk

• Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.

  PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 61

  Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC

  hct116 crc tumor chip-seq bulk single

• Heterogeneity and Differentiation Trajectories of Infiltrating CD8+ T Cells in Lung Adenocarcinoma.

  PMID 36358600 · PMC9658355 · Cancers · 2022 · 7 claims · 8 setups

  Has reproduction · 67

  Infiltrating CD8+ T cells in LUAD can be divided into ten transcriptionally distinct subsets: eight cytotoxic (CTL) subsets, one naive-like (NTL) subset, and one exhausted (ETL) subset.

  luad tcga cd8+ degs single-cell cibersort survival

• Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

  PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

  lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell

• Single-Cell Profiling Across Immune Tissues and Organs Reveals Immunosenescence Signatures in Male Rhesus Monkeys.

  PMID 41556329 · PMC13042567 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  GZMB is markedly upregulated across multiple cell types in aged rhesus monkeys and serves as a candidate biomarker of immunosenescence

  bone cd8+ mesenteric sections single-cell gene pseudotime

• A muscle-centered hierarchical breakdown underlies flight loss during silkworm domestication.

  PMID 41716997 · PMC12915254 · iScience · 2026 · 8 claims · 8 setups

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  Flight loss in B. mori results from a muscle-centered collapse of a three-tiered hierarchical genetic module comprising mitochondrial energy production (COX3/ND1), wing vein patterning (Dally/CtBP), and flight muscle specification (Yki)

  wing wings flight mandarina single-cell spatial velocity

• Role of CTGF-LRP1 in impaired healing of cesarean section incisions.

  PMID 41764198 · PMC13066582 · Nature communications · 2026 · 8 claims · 8 setups

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  A specific fibroblast subgroup (FB3) in niche tissue shows LRP1 deficiency associated with reduced extracellular matrix (ECM) synthesis capacity

  myometrium adjacent sections fibroblasts single-cell hematoxylin masson's

• KRT15 identified by scRNA-Seq and machine learning as stemness regulator and prognostic biomarker in ESCC.

  PMID 41907411 · PMC13018899 · iScience · 2026 · 8 claims · 8 setups

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  A malignant epithelial subpopulation (Cluster 0) with the highest CytoTRACE stemness potential and highest EMT activity exists in ESCC scRNA-seq data

  escc degs eca109 kyse180 scrna-seq machine immunohistochemistry

• Patient-derived kidney organoids recapitulate ADPKD and facilitate the identification of Rho pathway inhibitors as candidate therapeutics.

  PMID 41946363 · PMC13130689 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Multi-lineage adult renal organoids (MAROs) can be established directly from adult human kidney tissue and expanded long-term while retaining proximal tubule and collecting duct lineages

  maros patient-derived pkd_orgs bulk single-cell immunofluorescence

• Dynamics of severity-associated immune remodeling by granulocytes and macrophages in acute lung injury.

  PMID 42111184 · PMC13157102 · iScience · 2026 · 7 claims · 7 setups

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  Granulocytes expand while macrophages are depleted as ALI severity progresses from intermediate to late stage

  bronchoalveolar granulocytes granulocyte immune single-cell gene pseudotime

• Rtf1-dependent transcriptional pausing regulates cardiogenesis.

  PMID 41537425 · PMC12807453 · eLife · 2026 · 8 claims · 7 setups

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  Rtf1 activity is essential for differentiation of the myocardial lineage from mesoderm

  zebrafish embryo embryonic mescs crispr situ shrna

• BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

  PMID 41660012 · PMC12876259 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

  Full-text index only

  BMP and NODAL (TGF-β) paracrine signalling are key routes of intercellular communication that respectively enhance or diminish the totipotent-like cell (TLC) state in mouse ESCs

  escs esc scrna-seq cellchat differential

• Autocrine SFRP2 (secreted frizzled related protein 2) enhances lung myofibroblast fibrogenic activity by suppressing PINK1-mediated mitophagy initiation.

  PMID 41789512 · PMC13185440 · Autophagy · 2026 · 7 claims · 8 setups

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  SFRP2 is specifically highly expressed in myofibroblasts derived from fibrotic (IPF/BLM/TGFB1-induced) lung tissue

  lung pmlfs mrc5 single-cell bulk histology

• Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

  PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

  Full-text index only

  A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

  tcga-blca blca paired wgcna differential machine

• Reduced cartilage matrix stiffness in temporomandibular joint osteoarthritis impairs the functions of superficial zone chondrocytes via downregulation of CREB5-PLPP3 signaling.

  PMID 41870835 · PMC13009359 · Molecular biomedicine · 2026 · 7 claims · 8 setups

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  ECM stiffness (Young's modulus) is reduced in the superficial zone of condylar cartilage in TMJOA patients and in a rat UAC-induced TMJOA model

  condylar szc tmjoa nanoindentation single-cell bulk