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).

• Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

  PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

  Has reproduction · 90

  MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

  pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent

• A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes.

  PMID 16420688 · PMC1382211 · BMC genomics · 2006 · 7 claims · 4 setups

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  PBEC and KC SAGE libraries show approximately 80% overlap in expressed tags, indicating high similarity in gene repertoire

  bronchial keratinocytes pbec types sage rt-pcr

• Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.

  PMID 19890111 · PMC2787406 · The New England journal of medicine · 2009 · 8 claims · 8 setups

  Full-text index only

  Homozygous loss-of-function mutations in IL10RA or IL10RB cause severe early-onset enterocolitis

  consanguineous patients ebv-transformed pbmcs genetic-linkage single-nucleotide-polymorphism candidate-gene

• Predicting position along a looping immune response trajectory.

  PMID 30296270 · PMC6175499 · PloS one · 2018 · 8 claims · 5 setups

  Has reproduction · 98

  Looper is an automated computational method that identifies gene pairs that trace looping trajectories when plotted against each other in longitudinally sampled data

  monocytes blood pbmcs montreal microarray qrt-pcr topological

• 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

• 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

• Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

  PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

  Full-text index only

  Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

  blood pooled gene chip-chip conventional quantitative

• Antibody protein array analysis of the tear film cytokines.

  PMID 18677223 · PMC3786218 · Optometry and vision science : official publication of the American Academy of Optometry · 2008 · 7 claims · 4 setups

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  Tear fluid contains factors with affinity for plastic, capture antibodies, and IgG that create matrix effects profoundly impacting dot ELISA/array reliability

  tear normalized antibody 12-plex two-step

• Screening of Diagnostic Biomarkers and Immune Infiltration Characteristics Linking Rheumatoid Arthritis and Rosacea Based on Bioinformatics Analysis.

  PMID 39104909 · PMC11299729 · Journal of inflammation research · 2024 · 8 claims · 8 setups

  Has reproduction · 48

  277 co-expressed DEGs shared between RA and rosacea are enriched in immune processes and chemokine-mediated signaling pathways

  synovial rosacea co-expressed serum microarray weighted protein-protein

• Genetics and proteomics: deciphering gene association studies in critical illness.

  PMID 16934133 · PMC1750993 · Critical care (London, England) · 2006 · 8 claims · 8 setups

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  Most critical illnesses are complex traits (multifactorial), unlike single-gene Mendelian diseases.

  severe families caucasian tnf genetic linkage microarray

• Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

  PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

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  IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

  population blood genomic hapmap snp survival allele

• Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

  PMID 19859740 · PMC2939908 · Human genetics · 2010 · 7 claims · 7 setups

  Full-text index only

  NOS2 promoter haplotypes are not consistently associated with malaria severity or malarial anemia across three independent Tanzanian study populations

  tanzanian a549 muheza-tanga sscp pcr restriction

• How bacterial communities expand functional repertoires.

  PMID 17238278 · PMC1750926 · PLoS biology · 2006 · 8 claims · 7 setups

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  The human microbiome contains roughly 100 times as many genes as does the human genome

  bacteroides distal interleukin-10-deficient macrophages transcriptional metagenomic microbiota

• A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

  PMID 19864672 · PMC2793117 · The New England journal of medicine · 2009 · 7 claims · 7 setups

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  A homozygous CARD9 point mutation (Q295X, premature termination codon) is associated with autosomal recessive susceptibility to chronic mucocutaneous candidiasis.

  family patients peripheral-blood peripheral snp microsatellite sanger

• Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma: Transcriptional Signature and In Vitro Modeling.

  PMID 37958322 · PMC10650304 · Cancers · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  Reanalysis of scRNA-Seq identified 279 iMSC signature genes upregulated in BM MSCs of MM patients vs healthy donors, covering 82% of the top 50 previously defined iMSC genes

  facs-isolated mscs expanded single-cell bulk meta-analysis

• A surrogate-based approach for post-genomic partner identification.

  PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

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  Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

  biotinylated tnf-β analysis secondary phage sequence secondary

• Critical care: applying genomics to inflammation outcomes.

  PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

  Full-text index only

  Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

  leukocytes whole-blood healthy peripheral genomewide whole-genome microarray

• Gene-environment interaction and obesity.

  PMID 19019037 · PMC3683966 · Nutrition reviews · 2008 · 8 claims · 8 setups

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  Obesity susceptibility is largely genetically determined but requires environmental exposure (excess energy intake, low fiber, physical inactivity) to manifest phenotypically.

  framingham european individuals healthy genome-wide candidate gene-diet

• Update on diabetes mellitus.

  PMID 15502249 · PMC3839330 · Disease markers · 2004 · 8 claims · 7 setups

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  Type 1 diabetes results from selective destruction of pancreatic beta cells via T-cell and cytokine mediated autoimmune mechanisms, possibly involving destruction of peri-islet Schwann cells.

  nod t1dm islets 3t3-l1 seldi-tof tof two-dimensional

• New strategies in drug discovery.

  PMID 16671397 · PMC7120019 · Methods in molecular biology (Clifton, N.J.) · 2006 · 8 claims · 8 setups

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  A new integrated drug discovery paradigm has emerged combining clinical, genetic, genomic, and molecular phenotype data with cheminformatics, managed via informatics

  animal normal low-abundance mice situ microarray taqman