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 9

System / cell line: identified ✕ Assay: standard ✕ Clear

Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

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DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

standard dsic-labeled immunodepleted serum labeling quantitative in-solution
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition

standard thp-1 replicate lc-ms manual cross-instrument
Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 8 setups

Has reproduction · 19

Shared differentially expressed genes link glioblastoma with ischemic stroke and with moyamoya disease, revealing molecular associations among the diseases.

glioblastoma ischemic moyamoya shared bulk microarray gene
Mutations in NYX of individuals with high myopia, but without night blindness.

PMID 17392683 · PMC2642916 · Molecular vision · 2007 · 7 claims · 5 setups

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Two novel NYX missense mutations (Cys48Trp and Arg191Gln) were found in unrelated males with high myopia but no night blindness.

unrelated individuals high model direct sequencing electroretinogram
Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

PMID 19722698 · PMC2783519 · Journal of proteome research · 2009 · 7 claims · 6 setups

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Tandem IgY7-SuperMix separation nearly doubles overall proteome coverage compared to IgY7 flow-through alone (523 vs 263 confidently identified proteins)

plasma identified lc-ms sds-page spike-in
HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

PMID 18714345 · PMC2500163 · PloS one · 2008 · 7 claims · 4 setups

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HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.

t-cell identified gel maldi-tof bioinformatics
Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.

PMID 19834888 · PMC4302342 · Proteomics · 2009 · 7 claims · 7 setups

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BioCAT (biotin tagging + AACT) enables highly sensitive and accurate single-step screening of mammalian protein-protein interactions without establishing a stable cell line

293t standard nk92mi list western sds-page nanolc-ms
Benefit of using interaction effects for the analysis of high-dimensional time-response or dose-response data for two-group comparisons.

PMID 38012163 · PMC10682470 · Scientific reports · 2023 · 5 claims · 1 setups

Has reproduction · 92

Interaction effects are often the mathematical equivalent of the biological research question in gene expression studies but are frequently not considered in practice.

mice bulk
Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

PMID 19109909 · PMC2630178 · Neuron · 2008 · 8 claims · 8 setups

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MEF2 directly regulates a genome-wide program of 182 activity-dependent target genes in hippocampal neurons

e18 hippocampal forebrain profiling rt-qpcr chip-chip

Experiments

Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

Mutations in NYX of individuals with high myopia, but without night blindness.

Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.

Benefit of using interaction effects for the analysis of high-dimensional time-response or dose-response data for two-group comparisons.

Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.