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).

• Sox8 remodels the cranial ectoderm to generate the ear.

  PMID 35867760 · PMC9282420 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Sox8 sits at the top of a core transcriptional circuit (Sox8, Pax2, Lmx1a, Zbtb16) that determines otic identity

  chick bulk single-cell chipseq

• 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

  Full-text index only

  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

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

  Full-text index only

  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative

• KEGG for linking genomes to life and the environment.

  PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

  protein-coding newly microarray kegg sequence computational glycan

• Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.

  PMID 41560697 · PMC13042525 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  Mitochondrial somatic mutations from scRNA-seq can be repurposed as endogenous genetic barcodes for lineage tracing in hPSC-derived organoids.

  hpsc hemo larry-barcoded pdgfrα+ scrna-seq mitochondrial cospar

• 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

• Single-cell gene expression and TCR profiling reveal age-related differences in recent thymic emigrants.

  PMID 42023153 · PMC13098507 · iScience · 2026 · 8 claims · 5 setups

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  Neonatal and adult CD8+ RTEs are phenotypically and functionally distinct despite equivalent post-thymic maturation time

  splenic neonatal sorted flow single-cell differential

• A cell atlas of multiple liver organoids and the fetal liver based on scRNA-seq.

  PMID 41736863 · PMC12927097 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  A unified liver organoid cell atlas of 217,025 high-quality cells was constructed by integrating scRNA-seq data from 15 organoid samples across 9 studies with human fetal liver data (5-19 weeks gestation)

  liver fetal endoderm-derived mesoderm-derived scrna-seq pseudotime pearson

• AP-1 mediates cellular adaptation and memory formation.

  PMID 41862498 · PMC13168276 · Nature communications · 2026 · 8 claims · 7 setups

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  Cancer cells form and maintain cellular memories when becoming drug resistant, exhibiting cellular learning dependent on the transcription factor AP-1

  wm989 h2b-gfp h358 rna-seq atac-seq colony

• FOXP1 is differentially active during development of murine vasopressin and oxytocin magnocellular neurons.

  PMID 42088346 · PMC13138059 · iScience · 2026 · 8 claims · 7 setups

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  FOXP1 participates in MCN development and is differentially active in OXT MCNs relative to AVP MCNs

  hypothalamus hypothalamic avp neuro-2a single-cell gene fate

• Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

  PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

  immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime

• Mosaic partial epidermal reprogramming remodels neighbors and niches to refine skin homeostasis and repair.

  PMID 41617708 · PMC12960685 · Nature communications · 2026 · 8 claims · 8 setups

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  A genetically engineered mouse model (Krt14-CreER; LSL-rtTA-EGFP; TetO-OSKM-mCherry, 'Epi-iOSKM') enables transient, reversible, mosaic OSKM expression in interfollicular epidermal cells without inducing pluripotency or teratoma risk

  epidermis sorted epidermal ife immunostaining single-cell pseudotime

• Persistence of alveolar fibroblast-derived ADAMTS4+ cells in a preclinical model of delayed pulmonary fibrosis resolution.

  PMID 42103706 · PMC13156320 · Nature communications · 2026 · 8 claims · 8 setups

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  Lipofibroblasts (LIFs/AF1) differentiate into myofibroblasts during fibrogenesis, with the reverse (MyoFB-to-LIF) trajectory occurring during fibrosis resolution

  aged live facs-sorted scrna-seq h&e masson's rnascope

• Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs.

  PMID 41932885 · PMC13219436 · Nature communications · 2026 · 8 claims · 8 setups

  Has reproduction · 91

  A fraction (15-50%) of the distal SOX9+ tip progenitor subdomain is sufficient to direct lung outgrowth through branch bifurcation, providing a mechanism for lung size control

  lung whole-mount immunofluorescence single-cell

• Keratin 5 marks cancer-propagating cells sustained by an osteopontin-producing niche in high-grade serous ovarian carcinoma.

  PMID 42111394 · PMC13155427 · Cancer heterogeneity and plasticity · 2026 · 8 claims · 8 setups

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  KRT5+ cells represent bona fide cancer-propagating cells (CPCs) in HGSC

  hgsc skov3 facs-sorted nod immunohistochemistry lentiviral organoid