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).
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Estrogen Production in Pancreatic Cancer Shapes a Tumor-Suppressive Stromal Microenvironment.
PMID 41258799 · PMC12862343 · Cancer research · 2026 · 8 claims · 6 setups
Serum levels of stromal biomarkers associated with favorable outcomes were significantly higher in female patients with PDAC than in male patients
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Dextrorotatory kynurenine suppresses acute rejection through inhibiting M1 macrophage-mediated inflammation.
PMID 41644740 · PMC12988155 · EMBO molecular medicine · 2026 · 8 claims · 7 setups
Elevated serum D-Kyn levels correlate with stable graft function, while lower D-Kyn is associated with acute rejection
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Protocol for single-cell optimization objective and trade-off inference.
PMID 41790544 · PMC12992945 · STAR protocols · 2026 · 6 claims · 6 setups
SCOOTI is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs
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LIMCH1-enriched extracellular vesicles promote vascular permeability in early-onset preeclampsia.
PMID 41604492 · PMC12851021 · Science advances · 2026 · 8 claims · 8 setups
LIMCH1 is identified as an Eo-PE-associated EV protein via serum sEV proteomics combined with GEO placental transcriptome datasets
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Has reproduction · 95
Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.
PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 8 setups
Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells
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Has reproduction · 29
CD74 deficiency protects against doxorubicin cardiotoxicity through RRM2-mediated regulation of ferroptosis.
PMID 42180553 · PMC13198236 · Acta pharmaceutica Sinica. B · 2026 · 8 claims · 8 setups
CD74 levels are elevated in plasma of DOX-exposed breast cancer patients and in DOX-challenged mouse hearts and cardiomyocytes
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Has reproduction · 50
An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.
PMID 39209804 · PMC11362569 · Nature communications · 2024 · 7 claims · 7 setups
Human hepatocytes engrafted in liver chimeric mice display a large rhythmic transcriptome of ~1700 protein-coding orthologous genes, including transcription factors, chromatin modifiers, and metabolic enzymes.
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Has reproduction · 73
Vespucci: a system for building annotated databases of nascent transcripts.
PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups
Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.
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Annexin A13 Protects Against Acute Kidney Injury by Inactivating TGF-β/Smad3 Signaling.
PMID 41486854 · PMC12915081 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups
ANXA13 is selectively downregulated in the kidneys of AKI patients and IRI- or cisplatin-induced AKI mice, primarily in proximal tubular cells
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Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells.
PMID 41526192 · PMC12863184 · Genome research · 2026 · 8 claims · 6 setups
microRNAs form four distinct coexpression groups across single mESCs
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Has reproduction · 50
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
A post-stroke perivascular microglia niche (stroke-VAM) is identified, characterized by low M2 marker expression and elevated glycolysis, OXPHOS, and phagocytic activity
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Has reproduction · 86
Development of double-positive thymocytes at single-cell resolution.
PMID 33771202 · PMC8004397 · Genome medicine · 2021 · 7 claims · 8 setups
DP thymocytes can be classified into blast, rearrangement, and selection subtypes, distinguishable by surface markers CD2 and Ly6d
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Has reproduction · 78
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.
PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups
A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors
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Deciphering immune and cellular reprogramming during the progression from inflammatory bowel disease to colorectal cancer using multi-omics single-cell and spatial transcriptomics.
PMID 42001187 · PMC13122952 · Journal of translational medicine · 2026 · 8 claims · 5 setups
CEACAM5 is consistently upregulated across Crohn's disease and ulcerative colitis samples and links epithelial activation in IBD to tumorigenic processes in CRC
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Immune profiling in a living human recipient of a gene-edited pig kidney.
PMID 41507576 · PMC12823403 · Nature medicine · 2026 · 8 claims · 8 setups
Xenograft experienced early T cell-mediated rejection (Banff grade 2A) within 1 week post-transplant despite profound circulating T cell depletion, likely driven by subtherapeutic immunosuppression and residual CD8+ T cells in lymph nodes.
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Single-cell dissection of regulated cell death dynamics in ovarian aging.
PMID 41689119 · PMC13005338 · Journal of ovarian research · 2026 · 8 claims · 8 setups
The RCD landscape of ovarian aging had not previously been characterized at single-cell resolution
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Has reproduction · 59
Nucleosome regulatory dynamics in response to TGFβ.
PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups
SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.
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Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.
PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups
Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression
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Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups
Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes
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Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility.
PMID 41638211 · PMC13091097 · Cell systems · 2026 · 8 claims · 7 setups
A complex, intact gut microbiome is necessary for the steady-state transcriptional landscape of all major brain-resident cell types, with myelinating oligodendrocytes and immune cells showing the largest microbiome-dependent transcriptional response.