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).

Publications 1.3k Datasets 392.5k Experiments 36

System / cell line: a549 ✕ Clear

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

PMID 34168290 · PMC8225889 · Communications biology · 2021 · 8 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 metabolomics real-time western
Tumor suppressor in lung cancer 1 (TSLC1) alters tumorigenic growth properties and gene expression.

PMID 16083501 · PMC1208945 · Molecular cancer · 2005 · 8 claims · 8 setups

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Restoration of TSLC1 expression in A549 cells (yielding the 12.2 line) suppresses tumorigenic growth, markedly reducing cell expansion/proliferation rate.

a549 nsclc expansion wst-1 flow
Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

PMID 16789823 · PMC1513265 · PLoS genetics · 2006 · 8 claims · 8 setups

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K63-polyubiquitin chain formation protects human cells against translesion synthesis-induced mutations by promoting error-free recovery of blocked replication forks.

a549 western proliferation clonogenic
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

PMID 18980691 · PMC2612029 · BMC genomics · 2008 · 8 claims · 8 setups

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mtDNA depletion confers specific, shared gene expression profiles in A549 cells grown in culture and as xenografts

a549 growth oxygen mtdna
Mutations in the focal adhesion targeting region of deleted in liver cancer-1 attenuate their expression and function.

PMID 18829524 · PMC2597479 · Cancer research · 2008 · 8 claims · 6 setups

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The DLC-1 fragment spanning residues 201-500 is sufficient for focal adhesion targeting (FAT region)

a549 prostate colon mda-mb-468 immunofluorescence pcr colony
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
A high-temporal resolution technology for dynamic proteomic analysis based on 35S labeling.

PMID 18714357 · PMC2500177 · PloS one · 2008 · 6 claims · 6 setups

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35S pulse-labeling (phosphor-imaging) detects more protein spots with higher sensitivity than CBB staining on the same 2-DE gels

a549 liver 35s electrophoresis paired
Genome-scale modeling identifies dynamic metabolic vulnerabilities during the epithelial to mesenchymal transition.

PMID 39730911 · PMC11681178 · Communications biology · 2024 · 8 claims · 8 setups

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EMT involves temporal, stage-specific metabolic reprogramming with distinct dependencies in glycolysis and glutamine metabolism.

a549 recon1 cancer lung bulk single-cell genome-scale
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

Has reproduction · 67

PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

a549 sequence same bulk pathway gene
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

Has reproduction

The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional
Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

PMID 15502247 · PMC3839398 · Disease markers · 2004 · 8 claims · 8 setups

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Proteomics approaches (2D Western blot, protein microarray, multiplex ELISA) can identify tumor antigen-directed autoantibodies as candidate cancer biomarkers

lung pancreatic hepatocellular renal gel microarray multiplex
Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

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A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

carcinoma derivative xenograft custom quantitative
Use of functional genomics to understand influenza-host interactions.

PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

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Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

hela a549 lung texas cdna microarray infection
Proteomic identification of secreted proteins as surrogate markers for signal transduction inhibitor activity.

PMID 17211472 · PMC2360009 · British journal of cancer · 2007 · 5 claims · 5 setups

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Inhibiting EGFR signalling with Gefitinib alters the pattern of proteins secreted by cancer cells, and these changes can serve as an indirect quantitative assay for drug action

a431 a549 excised gel maldi-tof western
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
Cellular proteins in influenza virus particles.

PMID 18535660 · PMC2390764 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Purified influenza virions contain 36 host-encoded cellular proteins in addition to the 9 previously known viral proteins.

influenza deglycosylated sucrose lc-ms mudpit electron
Tubulin proteomics: towards breaking the code.

PMID 18840397 · PMC4039029 · Analytical biochemistry · 2009 · 8 claims · 8 setups

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Tubulin isotype and posttranslational-modification diversity constitutes a 'tubulin code' that is read by microtubule-associated proteins and translates into specific in vivo functions

bovine mda-mb-231 cancer a549 maldi-tof tandem sds-page
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

Has reproduction · 79

CLSM6A is a set of CNN-based deep learning models that predict single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

hct116 a549 brain hek293t miclip m6a-clip-seq m6a-seq
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
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 90

Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)

vero calu-3 genes direct pcr poly

Experiments

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

Tumor suppressor in lung cancer 1 (TSLC1) alters tumorigenic growth properties and gene expression.

Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

Mutations in the focal adhesion targeting region of deleted in liver cancer-1 attenuate their expression and function.

The cancer secretome: a reservoir of biomarkers.

A high-temporal resolution technology for dynamic proteomic analysis based on 35S labeling.

Genome-scale modeling identifies dynamic metabolic vulnerabilities during the epithelial to mesenchymal transition.

Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

Use of functional genomics to understand influenza-host interactions.

Proteomic identification of secreted proteins as surrogate markers for signal transduction inhibitor activity.

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

Cellular proteins in influenza virus particles.

Tubulin proteomics: towards breaking the code.

Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

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

Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.