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).

• Crunching the bio-numbers.

  PMID 14664241 · PMC1316909 · Environmental health perspectives · 2003 · 8 claims · 6 setups

  Full-text index only

  The eTag Assay System rapidly identifies genes and related proteins without complex sample preparation or follow-up bioinformatics, unlike microarrays

  blood model brain lung etag sirna addl

• Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

  PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 7 claims · 8 setups

  Has reproduction · 80

  C3 PLP2+ Tumor Epithelial Progenitor Cells are a key subpopulation that drives differentiation and progression of cervical carcinoma

  tumor tcga siha single-cell bulk rt-qpcr

• 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

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• Numb prevents a complete epithelial-mesenchymal transition by modulating Notch signalling.

  PMID 29187638 · PMC5721160 · Journal of the Royal Society, Interface · 2017 · 7 claims · 8 setups

  Has reproduction · 49

  Numb (and Numbl) inhibits a full EMT by stabilizing a hybrid E/M phenotype, acting as a 'phenotypic stability factor'.

  notch-emt-numb h1975 independent mathematical multi-cell sirna

• Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer.

  PMID 38435998 · PMC10909353 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 67

  TNBC can be classified into three molecular subtypes (clusters 1, 2, 3) based on cellular senescence-related pathways, with distinct prognoses (cluster 1 best, then 2, then 3).

  tnbc tcga-tnbc mda-mb-468 single-cell bulk copy

• Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.

  PMID 40936936 · PMC12420628 · Frontiers in immunology · 2025 · 7 claims · 8 setups

  Has reproduction · 71

  A highly stem-like C0 MAFF+ tumor cell subtype dominates invasive LUAD, producing chemokines and activating lipid metabolism

  luad tumor a549 single-cell infercnv pseudotime

• Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

  PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

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  APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

  magi pbmc 293t supt1 sensitive rt-pcr western

• Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

  PMID 15998458 · PMC1175981 · Genome biology · 2005 · 8 claims · 8 setups

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  The Schistosoma mansoni genome (~300 Mb) is nearing completion via whole-genome shotgun sequencing at ninefold coverage, with an estimated 15,000-20,000 protein-coding genes

  schistosoma brugia ancylostoma echinococcus whole-genome interference transgenesis

• LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

  PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 7 claims · 8 setups

  Has reproduction · 49

  LRP1 is the top hub gene with the highest diagnostic performance for distinguishing ectopic from eutopic endometrium in EMS

  ectopic geo training gwas microarray wgcna machine

• Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.

  PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 78

  KCTD16, CD3D and GSDMB are succinylation-related prognostic genes in BLCA

  paired tcga-blca geo gse135337 bulk single-cell rt-qpcr

• Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.

  PMID 33634984 · PMC7882098 · Clinical and translational medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  JMJD6 is an epigenetic vulnerability/fitness gene in RCC, identified by integrating GeCK CRISPR screening data with TCGA/ICGC RCC cohorts.

  tumor rcc 786-o balb crispr mtt sirna

• FOXM1 inhibitor, RCM‑1, enhances venetoclax mediated apoptosis through downregulation of ATP2B4 in rhabdomyosarcoma.

  PMID 41789627 · PMC12987556 · International journal of oncology · 2026 · 8 claims · 8 setups

  Has reproduction · 10

  Combination therapy of RCM-1 and venetoclax inhibits RMS tumor growth more efficiently than venetoclax alone in an animal model by decreasing proliferation and inducing apoptosis

  rms injected muscle cck-8 caspase subcutaneous

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

  PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

  normal dld1 beas2b ramos tss comparative

• Metabolomics applied to diabetes research: moving from information to knowledge.

  PMID 19875619 · PMC2768174 · Diabetes · 2009 · 8 claims · 7 setups

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  Metabolomics measures chemical phenotypes that are the net result of genomic, transcriptomic, and proteomic variability, providing the most integrated profile of biological status

  ins-1-derived pancreatic liver stedman 13c targeted ms-based

• RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

  PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

  airway asm most single rna-seq quantitative qrt-pcr

• Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.

  PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups

  Has reproduction · 96

  ID-seq combines antibody-based protein detection with DNA-sequencing of DNA-tagged antibodies to measure large numbers of (phospho-)proteins in many samples in parallel

  epidermal fixed skin differentiating id-seq immuno-pcr in-cell-western

• TGF-β-dependent reprogramming of amino acid metabolism induces epithelial-mesenchymal transition in non-small cell lung cancers.

  PMID 34168290 · PMC8225889 · Communications biology · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  TGF-β induces reprogramming of intracellular amino acid metabolism that is necessary to promote EMT in NSCLC cells

  a549 nsclc ce-tofms time-course real-time

• Unveiling the immunometabolic landscape of colorectal cancer through PANoptosis-related gene expression.

  PMID 41601652 · PMC12832467 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 41

  A CPAN-index prognostic model built from 11 PANoptosis-related differentially expressed genes (CPAN_DEGs) stratifies CRC patients into high-risk and low-risk groups with distinct survival and immunophenotypes.

  crc merged hct116 bulk single-cell immune