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).

• Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.

  PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 8 claims · 6 setups

  Has reproduction · 65

  UC patient-derived epithelial organoids histologically phenocopy primary UC tissue, while non-IBD organoids resemble healthy colonic epithelium.

  patient-derived h3k27ac histology immunohistochemistry bulk

• 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

• Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.

  PMID 19889237 · PMC2783166 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  scNT-MUC exhibit complete occlusive thrombi and absence of columnar epithelial layers not seen in control or scNT-N umbilical cords

  umbilical porcine puvec histology immunostaining real-time

• 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

• Loss of mutual protection between human osteoclasts and chondrocytes in damaged joints initiates osteoclast-mediated cartilage degradation by MMPs.

  PMID 34811438 · PMC8608887 · Scientific reports · 2021 · 6 claims · 8 setups

  Has reproduction · 50

  Human osteoclasts can differentiate on acellular cartilage, express osteoclast markers, and degrade cartilage matrix in a contact-dependent manner without forming F-actin rings or resorption pits.

  knee cd14+ osteoclasts conditioned histology osteoclast gag

• Differences in the histological findings, phenotypic marker expressions and genetic alterations between adenocarcinoma of the gastric cardia and distal stomach.

  PMID 17262083 · PMC2360051 · British journal of cancer · 2007 · 8 claims · 6 setups

  Full-text index only

  C-Ca is associated with a significantly higher incidence of differentiated-type tumours and lymphatic vessel invasion (LVI) compared with D-Ca

  resected c-ca microdissected formalin-fixed histopathological immunohistochemistry pcr-single-strand

• A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

  PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups

  Has reproduction · 83

  The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.

  intestine colon dss distal bulk phenotypic h&e

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• TFEB deficiency attenuates mitochondrial degradation upon brown adipose tissue whitening at thermoneutrality.

  PMID 33516944 · PMC7903014 · Molecular metabolism · 2021 · 7 claims · 8 setups

  Has reproduction

  BAT whitening at thermoneutrality is associated with TFEB-dependent mitochondrial degradation.

  bat subscapular tfeb-bat-ko metabolically qrt-pcr western immunohistochemistry

• Application of functional genomics to primate endometrium: insights into biological processes.

  PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

  Full-text index only

  Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

  endometrial uterus whole-genome cdna oligonucleotide

• The mouse gastric surface epithelial cell and its response to early Helicobacter pylori infection.

  PMID 41824631 · PMC13020875 · Virulence · 2026 · 8 claims · 5 setups

  Has reproduction · 100

  LCM followed by RNA-Seq is a feasible methodology for characterizing gastric SMCs and their host response to H. pylori infection in vivo

  c57bl gastric ffpe rna-seq mass immunofluorescence

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal

• A DNA microarray survey of gene expression in normal human tissues.

  PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

  Full-text index only

  Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

  normal common computational each two-color comparative unsupervised

• Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

  PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 6 claims · 8 setups

  Has reproduction

  A deep learning WSI cluster (three-class mini batch K-means on Inception V3 features) is associated with overall survival (P<0.001) and is an independent prognostic predictor (P=0.031) in BLCA.

  tcga-blca blca tcga deep transfer-learning neural-network

• Transcription-terminating mutation in telethonin causing autosomal recessive muscular dystrophy type 2G in a European patient.

  PMID 18948002 · PMC2592511 · Neuromuscular disorders : NMD · 2008 · 7 claims · 7 setups

  Full-text index only

  The patient carries a homozygous Trp25X (TGG→TGA) mutation in TCAP causing premature termination of translation/transcription and complete telethonin deficiency.

  pelvis skeletal muscle genomic muscle histology electron

• 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

• 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

• 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

• comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

  PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups

  Has reproduction · 65

  comBO is a single iPSC differentiation generating lymphoid, myeloid, vascular, mesenchymal stromal, and functional osteo/adipogenic lineages within one organoid

  ipsc-derived combo combo-derived mscarlet-tagged flow single-cell confocal

• 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

  Has reproduction · 50

  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.

  liver hcv-infected serum bulk chip-seq serum