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).

• Pathway-targeting gene matrix for Drosophila gene set enrichment analysis.

  PMID 34710184 · PMC8553153 · PloS one · 2021 · 8 claims · 4 setups

  Has reproduction · 95

  Gene matrix files for GSEA are largely unavailable for Drosophila, limiting pathway-level enrichment analysis in this model organism

  drosophila reactome kegg gene fluorescence manual

• 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

• GeneTrail--advanced gene set enrichment analysis.

  PMID 17526521 · PMC1933132 · Nucleic acids research · 2007 · 8 claims · 2 setups

  Full-text index only

  GeneTrail is a comprehensive, easy-to-use web-based tool for gene set enrichment analysis supporting both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA)

  example sorted over-representation gene

• Antigen and checkpoint receptor engagement recalibrates T cell receptor signal strength.

  PMID 34534438 · PMC8585507 · Immunity · 2021 · 6 claims · 7 setups

  Has reproduction · 37

  TCR signal strength drives dynamic, dose- and time-dependent transcriptional changes in CD4+ T cells while single-cell Nr4a3 activation dynamics remain digital/uniform.

  tg4 sorted live melanoma flow rna-seq re-stimulation

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils.

  PMID 33948572 · PMC8080108 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 35

  Neutrophils recruited to CF airways undergo rapid, broad transcriptional firing that upregulates anabolic genes and downregulates antimicrobial genes

  blood healthy transmigrated cfasn-transmigrated flow transmigration content