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).

• Quantitative mass spectrometry of diabetic kidney tubules identifies GRAP as a novel regulator of TGF-beta signaling.

  PMID 19836472 · PMC2829334 · Biochimica et biophysica acta · 2010 · 8 claims · 7 setups

  Full-text index only

  Label-free 2D-LC-MS/MS quantitative proteomics identified 476 significantly differentially expressed proteins in kidney tubules of diabetic OVE26 mice versus control mice

  kidney hk11 list 2d-lc-ms immunoblot immunohistochemistry

• The impact of microRNAs on protein output.

  PMID 18668037 · PMC2745094 · Nature · 2008 · 8 claims · 8 setups

  Full-text index only

  MicroRNA targeting for protein repression occurs primarily through seed-matched sites (6mer, 7mer-A1, 7mer-m8, 8mer) located in favourable predicted contexts within 3′ UTRs

  hela neutrophils bone mir-223 quantitative blot microarray

• Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

  PMID 33722289 · PMC7962346 · Genome biology · 2021 · 6 claims · 7 setups

  Has reproduction · 66

  A PE2-mediated single-base (C>G) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder but not heart or brain, mirroring HDR-mediated 3-bp substitution.

  zygotes aorta genomic aortae crispr prime quantitative

• Effects of Pharmacological Thermogenic Adipocyte Activation on Metabolism and Atherosclerotic Plaque Regression.

  PMID 30813320 · PMC6412269 · Nutrients · 2019 · 8 claims · 7 setups

  Has reproduction

  Chronic dietary CL316,243 treatment reduces adiposity and enhances body weight loss independent of food intake in LDLR-deficient mice

  ldlr-deficient bat ingwat liver body histology quantitative

• Intact innervation is essential for diet-induced recruitment of brown adipose tissue.

  PMID 30576247 · PMC6459298 · American journal of physiology. Endocrinology and metabolism · 2019 · 8 claims · 6 setups

  Has reproduction

  Intact innervation of BAT is essential for diet-induced thermogenesis/recruitment.

  interscapular whole-body adipose ibat surgical indirect western

• 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

• Ligilactobacillus salivarius regulating translocation of core bacteria to enrich mouse intrinsic microbiota of heart and liver in defense of heat stress.

  PMID 40276518 · PMC12018310 · Frontiers in immunology · 2025 · 7 claims · 6 setups

  Has reproduction

  Intrinsic microbiota (chiefly genera Burkholderia and Ralstonia) reside in the heart and liver of SPF mice, with the heart having lower bacterial abundance than the liver

  spf heart ileum metagenomic culturomics 16s

• Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

  PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

  Full-text index only

  Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

  liver genomic hcv-infected agilent two-color semi-quantitative real-time

• RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

  PMID 36429012 · PMC9688714 · Cells · 2022 · 6 claims · 7 setups

  Has reproduction · 37

  RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression.

  brain naïve wild-type spinal editing quantitative eae

• IL-6 trans-Signaling Regulates Neutrophilic Inflammation in Alcohol-Associated Hepatitis.

  PMID 40562277 · PMC13168973 · The American journal of pathology · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  Hepatic IL-6R expression progressively declines with increasing severity of alcohol-related liver disease, from normal to early ASH to nonsevere and severe AH

  liver hepatocytes hepg2 ptpn11 bulk immunohistochemistry single-cell

• Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

  PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 7 claims · 8 setups

  Has reproduction · 64

  Dgat2 is a novel mitochondria-related gene target and biomarker for myocardial ischemia-reperfusion injury

  cardiac frozen c57bl serum microarray rt-pcr western

• Metabolic syndrome: from epidemiology to systems biology.

  PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

  populations rats adipose four genome-wide linkage gene

• Transcriptome profiling of osteoclast subsets associated with arthritis: A pathogenic role of CCR2(hi) osteoclast progenitors.

  PMID 36591261 · PMC9797520 · Frontiers in immunology · 2022 · 8 claims · 6 setups

  Has reproduction · 50

  CCR2hi and CCR2lo periarticular bone marrow OCP subsets show a disparate transcriptome (863 differentially expressed genes)

  sorted rna-seq periarticular bulk gene flow

• Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.

  PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity

  lung c57bl pbmcs macrophages bulk metabolomics histopathology

• CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

  PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

  Full-text index only

  CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

  neuroblastoma nlf athymic methylation-specific quantitative soft

• Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

  PMID 18443592 · PMC2742198 · Nature genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Osteoglycin (Ogn) is a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM

  heart ogn cos-1 neonatal eqtl quantitative genome-wide

• Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

  PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

  Full-text index only

  A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

  carcinoma derivative xenograft custom quantitative

• The many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• Liver-specific paraoxonase-1 alleviates regulatory T cell-driven immunosuppression via metabolic reprogramming in hepatocellular carcinoma.

  PMID 41387425 · PMC12701056 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  PON1 expression is downregulated in HCC tumor tissue and low PON1 is associated with worse prognosis

  hcc paired hepa1-6 pon1-nc bioinformatic immunohistochemistry orthotopic

• Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.

  PMID 41345108 · PMC12789597 · Nature communications · 2025 · 7 claims · 8 setups

  Has reproduction · 93

  SIRT6 is an evolutionarily conserved regulator of tryptophan catabolism that balances tryptophan usage between the kynurenine and serotonin/melatonin pathways

  embryonic brains sirt6 serum untargeted rna-seq microarray