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).

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

  mammary surgically normal single-cell whole-mount integration

• Stromal androgen signaling acts as tumor niches to drive prostatic basal epithelial progenitor-initiated oncogenesis.

  PMID 36323713 · PMC9630272 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Loss of AR in stromal Gli1-lineage cells diminishes prostate epithelial oncogenesis and tumor development in vivo

  ugm hi-myc prostate hmyctg+ genetically single-cell immunohistochemistry

• Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

  PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

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  Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

  luad pan-cancer tumor scrna-seq spatial bulk

• Targeting TPX2-dependent lineage plasticity by CDK4/6 inhibition reverses therapy resistance in neuroendocrine bladder carcinoma.

  PMID 41923619 · PMC13130694 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A 315-gene 'NE-like signature' (NE-like Sig), derived from the WGCNA MEmidnightblue module, marks a lineage-plasticity-associated transcriptional program distinct from canonical NE differentiation.

  cases in-house bladder nebc wgcna single-cell spatial

• Functional human salivary gland organoids for tissue regeneration in chemically defined culture systems.

  PMID 41707649 · PMC12923968 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A chemically defined, Matrigel-free complete medium (CM) generates hSGOs with more cohesive spheroid morphology, organized epithelial layers, and improved apical polarization compared to keratinocyte medium (KM-S) or Matrigel-embedded conditions

  submandibular smg-derived hsgos smg bright-field h&e single-factor

• Dual mechanisms of supporting cell regeneration in the neonatal mouse cochlea.

  PMID 41867623 · PMC13000480 · iScience · 2026 · 8 claims · 8 setups

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  GER cells regenerate IPhCs through both mitotic and non-mitotic mechanisms

  neonatal lgr5dtr ki67creert2 epcam+ whole-mount edu genetic

• Characterizing gene perturbations in single cells via network divergence analysis.

  PMID 41965857 · PMC13249949 · Nature communications · 2026 · 8 claims · 8 setups

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  scDNS quantifies gene-specific functional perturbations by measuring Jensen-Shannon divergence between condition-specific gene interaction network configurations

  ipsc-derived embryonic panc-1 triple scrna-seq single-nucleus

• Pulmonary organoid models demonstrate compositionally driven epithelial plasticity and immune polarization.

  PMID 41940331 · PMC13049529 · iScience · 2026 · 8 claims · 7 setups

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  Cellular composition at seeding (PD vs. BAL vs. Mixed) directs epithelial fate and immune polarization in organoid culture

  lung day organoid epithelial scrna-seq brightfield h&e

• Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.

  PMID 41537454 · PMC12805614 · The Journal of pathology · 2026 · 6 claims · 7 setups

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  snRNA-seq identifies a novel tenogenic heterologous differentiation program (SCX, MKX, TNMD) in an endometrial carcinosarcoma

  ffpe sections tumor cs4 single-nucleus immunohistochemistry fluorescence

• Neural network-assisted RNA velocity imputation for empowering transcript dynamics-based analyses.

  PMID 41736867 · PMC12927306 · iScience · 2026 · 8 claims · 8 setups

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  NARVI, a deep neural network trained on expression-velocity relationships of passed genes, can impute RNA velocity for dropped genes that conventional tools (e.g., scVelo, UniTVelo) fail to calculate

  hematopoietic lung erythroid bone scrna-seq cross-validation

• 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

• Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

  PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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  A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

  pca malignant tcga mda single-cell infercnv pseudotime

• Precancerous niche remodelling dictates nascent tumour persistence.

  PMID 41781610 · PMC13148994 · Nature · 2026 · 8 claims · 8 setups

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  Newly emerging tumours actively remodel their surrounding stroma into a 'precancerous niche' that determines their long-term survival.

  upper nascent oesophagus carcinogen-free immunofluorescence edu immune

• A comprehensive multi-omics and functional study of evolutionary adaptive responses to smoke.

  PMID 42016314 · PMC13092862 · iScience · 2026 · 7 claims · 8 setups

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  A 'smoking signature' of 195 upregulated and 35 downregulated genes distinguishes current from never smokers in bronchial biopsies and validates across independent in vitro ALI datasets

  bronchial air-liquid lung n=12 bulk gsva spatial

• 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

• miR-203 facilitates timely cell fate transitions via epigenetic modulation during early embryogenesis.

  PMID 41811946 · PMC12978216 · Science advances · 2026 · 8 claims · 8 setups

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  miR-203 is required for a timely totipotency-to-pluripotency transition during early mouse embryogenesis

  preimplantation 8-cell mice mir-203 qrt-pcr genotyping time-lapse