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).

• GSDME-mediated pyroptosis promotes the progression and associated inflammation of atherosclerosis.

  PMID 36807553 · PMC9938904 · Nature communications · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  GSDME-mediated pyroptosis promotes atherosclerosis progression and its associated inflammation

  carotid macrophages gsdme− apoe− single-cell transmission immunohistochemistry

• Enteroendocrine cell lineages that differentially control feeding and gut motility.

  PMID 36810133 · PMC10032656 · eLife · 2023 · 6 claims · 8 setups

  Has reproduction · 88

  Vil1-p2a-FlpO knock-in mice combined with lineage-specific Cre lines enable highly selective intersectional genetic access to major enteroendocrine cell lineages (serotonin/enterochromaffin, GLP1, CCK, somatostatin, GIP) in vivo

  neurod1-cre neurog3-cre intestinal vil1-p2a-flpo single-cell fluorescence-activated two-color

• Microglial Fkbp5 Impairs Post-Stroke Vascular Integrity and Regeneration by Promoting Yap1-Mediated Glycolysis and Oxidative Phosphorylation.

  PMID 41355597 · PMC13042415 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A post-stroke perivascular microglial niche (stroke-VAM) exists, characterized by low M2 marker expression and elevated glycolysis, OXPHOS, and phagocytic activity.

  ipsilateral cx3cr1cre peri-infarct ischemic single-cell single-nucleus immunofluorescence

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 78

  INVADE-seq simultaneously captures host and bacterial transcripts to map bacteria-host interactions across diverse testicular cell types at single-cell resolution

  testes testis young testicular invade-seq histology sperm

• Identification and Mechanisms of Osteocyte Subsets Involved in the Pathological Progression of Osteoporosis.

  PMID 41250977 · PMC12850396 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Has reproduction · 57

  Six distinct osteocyte subsets (C1-C6) exist in mouse bone, identified by single-cell sequencing.

  femoral dmp1-cre+ sorted bmdms single-cell flow western

• Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

  PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

  Has reproduction · 55

  Microglia, endothelial cells, and pericytes exhibit the highest type I interferon (IFN-I) activity among PD midbrain cell types, with microglia showing markedly higher activity in PD.

  midbrain microglia substantia mptp-induced single-cell gene bulk

• Phased differentiation of γδ T and T CD8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers.

  PMID 34721945 · PMC8555559 · Oncoimmunology · 2021 · 8 claims · 6 setups

  Has reproduction · 44

  In tumors, infiltrating γδ T cells (predominantly TCRVγnon9) are quantitatively correlated with and aligned to CD8 T cells for differentiation, exhaustion, gene expression, and response to immune checkpoint therapy.

  splenic healthy tumor syngeneic single-cell scrnaseq citeseq

• Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation.

  PMID 37602956 · PMC10548174 · The EMBO journal · 2023 · 6 claims · 5 setups

  Has reproduction · 91

  E14.5 DFPs have a repressed transcriptional profile marked by high H3K27me3 and inaccessible chromatin at lineage-specific genes

  skin dermal single-cell chamber chip-seq

• 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

• Monocytes serve as Shiga toxin carriers during the development of hemolytic uremic syndrome.

  PMID 39871175 · PMC11773931 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  Monocytes are the primary carriers that transport Stx2 from the periphery to the kidney during STEC-induced HUS

  peripheral thp-1 cfse-labeled evs single-cell flow toxin-cell

• Distinct sympathetic projections to brown fat regulate thermogenesis and glucose tolerance.

  PMID 41559445 · PMC12945688 · Nature metabolism · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Distinct sympathetic neuron subpopulations in the stellate ganglion (SG) innervating iBAT parenchyma versus its vasculature mediate separable functions of the depot.

  th-cre awake ibat plasma retrograde chemogenetic indirect

• Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

  PMID 37081150 · PMC10154250 · Nature immunology · 2023 · 8 claims · 6 setups

  Has reproduction · 37

  Orthogonal engineering of CD8+ T cells to co-secrete IL-2v and IL-33 (with PD-1 decoy) drives a novel synthetic effector state (C5 T_SE) that deviates from canonical PD-1+TOX+ exhaustion.

  ot1 b16-ova facs-sorted engineered adoptive flow single-cell

• Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.

  PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups

  Has reproduction · 83

  Mural cell-derived chemokines CCL2 and MIF preserve vascular macrophage survival and homeostatic function, generating a protective niche.

  cx3cr1-mφca-rep mcrfp-rep cx3cr1-mφgfp-rep peritoneal multi-photon confocal imaging

• D2H2: diabetes data and hypothesis hub.

  PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 5 setups

  Has reproduction

  D2H2 is a web portal hosting hundreds of curated, uniformly reprocessed diabetes-relevant transcriptomics datasets from GEO with per-study visualization, differential expression, and single-gene queries.

  obese type pubmed bulk single-cell single-gene

• Why an integrated view of gene expression studies on hematopoiesis in mouse aging is better than the sum of their parts.

  PMID 38627103 · PMC11586588 · FEBS letters · 2024 · 7 claims · 4 setups

  Has reproduction · 75

  Combining differentially expressed (DE) gene lists from multiple publications into a unified 'aging list' (AL) with citation counts, and deriving a shorter high-confidence 'aging signature' (AS, genes cited in >3 publications, ~200 genes), produces a more reliable and consistent picture of hematopoietic aging than any single study.

  hematopoietic compiled gene bulk single-cell

• Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles.

  PMID 29907695 · PMC6068466 · The EMBO journal · 2018 · 8 claims · 8 setups

  Has reproduction · 46

  B16F1 and B16F10 melanoma subclones functionally exchange EVs in vivo, transferring Cre mRNA cargo detectable via a Cre-LoxP color-switch reporter system

  co-injected b16f1 locally 16.5k intravital cre-loxp rt-pcr

• Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.

  PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 6 claims · 7 setups

  Has reproduction · 100

  A distinct gene co-expression module with a prominent T cell signature is enriched in unstable plaques and distinguishes high-risk from low-risk lesions.

  carotid calcified atherosclerotic cell-specific microarray single-cell loss-of-function

• Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.

  PMID 34719737 · PMC8629906 · Cellular and molecular life sciences : CMLS · 2021 · 7 claims · 8 setups

  Has reproduction · 50

  VAP-1 is expressed on a subset of human HSC and on bone marrow vasculature, forming a hematogenic niche.

  facs-sorted sorted cd34+ bulk single-cell flow

• Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

  PMID 11879542 · PMC128918 · Arthritis research · 2002 · 8 claims · 6 setups

  Full-text index only

  Antibody sequences that violate normal ontogenic/developmental constraints indicate a failure of B-cell regulation

  peripheral diseased rheumatoid autoimmune immunoglobulin single-cell cloning

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

  PMID 36323713 · PMC9630272 · Nature communications · 2022 · 7 claims · 7 setups

  Has reproduction · 63

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

  ugm hi-myc prostate hmyctg+ genetic single-cell gene