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).

• 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

• Machine learning-driven transcriptomic and single-cell profiling of programed cell death patterns in colon cancer.

  PMID 41854308 · PMC13009810 · Science progress · 2026 · 8 claims · 8 setups

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  Disulfidptosis and anoikis are consistently identified as the most robust prognostic PCD patterns in colon cancer across six independent machine learning algorithms

  colon coad ssgsea-based machine differential

• Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

  PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein

• Protocol for generating and characterizing Matrigel-free prostate cancer patient-derived organoids.

  PMID 41955100 · PMC13091043 · STAR protocols · 2026 · 7 claims · 7 setups

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  A Matrigel-free culture protocol improves both take-rate and proportion of tumor cells within PCa PDO cultures compared to traditional Matrigel-based approaches

  pca turp ffpe organoid serial frozen

• Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer.

  PMID 41723121 · PMC12932787 · Nature communications · 2026 · 8 claims · 8 setups

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  Different tumor cell transcriptomic states organize into distinct spatial clusters, or 'villages', each supported by a unique surrounding microenvironment

  liver malignant non-malignant tumor single-cell immunofluorescence non-negative

• Pharmacogenomic screening identifies and repurposes leucovorin and dyclonine as pro-oligodendrogenic compounds in brain repair.

  PMID 39537633 · PMC11561360 · Nature communications · 2024 · 8 claims · 8 setups

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  A pharmacogenomic scoring strategy (OligoScore) combining transcriptomic signatures and curated oligodendrogenesis gene sets identifies compounds with pro-oligodendrogenic transcriptional activity

  brain neonatal gene cerebellar bulk transcriptomic pharmacogenomic

• Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

  PMID 41555918 · PMC12812404 · Frontiers in genetics · 2025 · 7 claims · 5 setups

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  LiVAE, a dual-pathway VAE with Lorentzian geometric regularization between a primary Euclidean pathway and an information-bottleneck pathway, balances local fidelity with global topology coherence in single-cell embeddings

  single-cell same dapp1 benchmarking umap component-wise

• pmid-42010620

  PMID 42010620 · PMC13227897 · 8 claims · 5 setups

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  Morphine-dependent macaques show increased CD4+ TCM and Treg cell proportions and decreased CD8+ TEM cell proportions in CSF at the pre-infection timepoint compared to saline controls

  csf scrna-seq necropsy single-cell flow cell-cell

• Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.

  PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 7 setups

  Has reproduction · 49

  S100A3 shows consistent discriminatory performance across the training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort

  blood degs bulk single-gene gene

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution.

  PMID 41895263 · PMC13106970 · Cell reports methods · 2026 · 8 claims · 5 setups

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  scRNA-seq references yield significantly higher Pearson correlation and lower RMSE than snRNA-seq references for deconvolution across all four tissue datasets

  adipose same fat-cell real pseudobulk single-cell synthetic

• Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

  PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

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  HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.

  hr+ epcam-sorted tumor tcga-brca droplet sidr-seq bulk

• Cytoplasmic LIM domain only 2 enhances tumor endothelial cell migration through integrin β1-mediated focal adhesion signaling.

  PMID 41639897 · PMC12983546 · Acta neuropathologica communications · 2026 · 8 claims · 8 setups

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  LMO2 is highly expressed in tumor-associated vasculature/endothelial cells compared with normal brain vasculature

  glioblastoma orthotopic huvecs huvec-lmo2 single-cell transcriptomic immunofluorescence

• Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.

  PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types

  bulk py2t mcf10a airway transcriptomic rna-seq single-cell

• Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

  PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

  Has reproduction · 50

  Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

  hnscc tcga-hnscc caf fibroblast single-cell bulk spatial

• DHODH links mitochondrial bioenergetics, one-carbon metabolism, and DNA repair to sustain aggressive prostate adenocarcinoma.

  PMID 41612476 · PMC12930642 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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  DHODH is markedly overexpressed in malignant prostate epithelial cells and abundant in tumors

  tcga-prad gse141445 22rv1 bulk single-cell lentiviral

• 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

• POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

  PMID 41645751 · PMC12891935 · Oncology reports · 2026 · 8 claims · 8 setups

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  Integration of two HNSCC scRNA-seq datasets reveals two distinct fibroblast subtypes: POSTN- and POSTN+ fibroblasts

  hnscc tcga-hnscc oscc oscc-derived single-cell bulk immunohistochemistry

• Spatial single-cell analysis reveals tumor microenvironment signatures predictive of oral cavity cancer outcome.

  PMID 41707652 · PMC12923947 · Cell reports. Medicine · 2026 · 8 claims · 6 setups

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  Proliferating (KI67+) PROX1+ lymphatic endothelial cells (LECs) at the tumor invasive margin are a strong independent adverse prognostic factor for recurrence-free and overall survival in early-stage OSCC

  ffpe lymphatic representative oscc imaging ki67+prox1+ transcriptomic