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).

• 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

• Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs.

  PMID 41932885 · PMC13219436 · Nature communications · 2026 · 8 claims · 8 setups

  Has reproduction · 91

  A fraction (15-50%) of the distal SOX9+ tip progenitor subdomain is sufficient to direct lung outgrowth through branch bifurcation, providing a mechanism for lung size control

  lung whole-mount immunofluorescence single-cell

• Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

  PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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  Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

  lung scanned excised peptide 2-d 2-de maldi-tof-ms

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.

  PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).

  lung covid-19 interaction pre-clinical composite single-cell kaplan-meier

• Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

  PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

  Full-text index only

  Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

  lung wild-type matched paired two-round real-time airs-rflp

• The cancer secretome: a reservoir of biomarkers.

  PMID 18796163 · PMC2562990 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Cancer secretome analysis is a promising reservoir for identifying novel, non-invasive cancer biomarkers, addressing limitations of whole blood/serum proteomics

  a549 m-be sw480 neoplastic 2-de dige icat

• Phosphoproteomics: unraveling the signaling web.

  PMID 18922462 · PMC2754874 · Molecular cell · 2008 · 8 claims · 8 setups

  Full-text index only

  Integrating discovery-based MS phosphoproteomics with targeted protein microarray technologies yields a more complete picture of signaling networks and improves clinical translation of findings.

  ddr atr-deficient hela mammary phosphospecific phospho-motif scx

• Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

  PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

  Full-text index only

  LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

  surgically tryptic set lysates lc-ms mascot immunohistochemistry

• Understanding the mechanisms of drug-associated interstitial lung disease.

  PMID 15340376 · PMC2750813 · British journal of cancer · 2004 · 8 claims · 7 setups

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  Apoptosis of alveolar/bronchial epithelial cells via Fas-FasL and mitochondrial (cytochrome c/caspase-9) pathways is a key mechanism underlying drug-, chemotherapy-, and radiation-associated lung injury and fibrosis

  bronchial lung swiss mice immunohistochemistry toxicology pulmonary

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 8 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm/pSHF via an evolutionarily conserved intronic enhancer.

  micro-dissected dissected e9.5 xenopus bulk rt-qpcr whole-mount

• The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease.

  PMID 38839750 · PMC11153611 · Nature communications · 2024 · 8 claims · 8 setups

  Has reproduction · 70

  Intestinal epithelial cell-specific deletion of Slc39a8 causes systemic manganese (Mn) deficiency in blood and multiple organs.

  c57bl frozen tissues slc39a8-iec qpcr immunofluorescence icp-ms

• 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

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• Identification of biofilm-associated cluster (bac) in Pseudomonas aeruginosa involved in biofilm formation and virulence.

  PMID 19065261 · PMC2587700 · PloS one · 2008 · 8 claims · 8 setups

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  A ΔpA3731 mutant is highly biofilm-defective on abiotic (polystyrene) and biotic (A549 pneumocyte) surfaces compared with wild-type PAO1

  aeruginosa a549 lung crystal biofilm adhesion

• New perspectives on an old disease: proteomics in cancer research.

  PMID 17472735 · PMC1895992 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  The HUPO Plasma Proteome Project has catalogued over 3,020 non-redundant gene products (>7,000 proteins/isoforms) in human plasma, many originating from tissues/organs rather than being plasma-intrinsic.

  plasma breast tumor genetically shotgun proteomics glycopeptide

• A new era for proteomics research?

  PMID 19014405 · PMC2614486 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Refined mass spectrometry instrumentation and software now make whole-proteome coverage of model organisms in a single experiment conceivable

  proteins lines kinases breast mass silac kinase-specific