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 14

System / cell line: labeled ✕ Assay: antibody ✕ Clear

The Proteomic Code: a molecular recognition code for proteins.

PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide
Autoantibody profiling for the study and treatment of autoimmune disease.

PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups

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Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.

serum antigen-antibody antigens fetal spotted elisa microarray
Stable isotope labeling tandem mass spectrometry (SILT): integration with peptide identification and extension to data-dependent scans.

PMID 18774841 · PMC2707264 · Journal of proteome research · 2008 · 8 claims · 5 setups

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Using MS/MS ion intensities with stable isotope labeling (SILT) decreases the effects of contamination from unrelated co-eluting compounds compared to precursor ion intensity methods.

astrocytes hepg2 app695δnl labeled nano-lc sds-page immunoprecipitation
Next-generation high-density self-assembling functional protein arrays.

PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

test high-density amine-coated array picogreen anti-gst fluorescently
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 74

ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
Pharmaco-proteomic study of hydroxyurea-induced modifications in the sickle red blood cell membrane proteome.

PMID 18849548 · PMC4260454 · Experimental biology and medicine (Maywood, N.J.) · 2008 · 6 claims · 6 setups

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50 μM HU treatment of SS RBC membranes causes statistically significant changes in a discrete set of membrane proteins, distinct from HbF induction.

sickle rbc excised 2d-dige tandem immunoblot
Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter.

PMID 18384686 · PMC2359743 · BMC cell biology · 2008 · 8 claims · 8 setups

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β1Int-HaloTag fusion protein localizes to the cell membrane in a pattern similar to endogenous β1 integrin, indicating the fusion does not disrupt normal integrin surface expression

hela hek293 live immunocytochemistry live fluorescence
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
Applying proteomics to the diagnosis and treatment of ALS and related diseases.

PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

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Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

csf spinal biofluid muscle 2d-dige antibody luminex
Monocytes serve as Shiga toxin carriers during the development of hemolytic uremic syndrome.

PMID 39871175 · PMC11773931 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

Has reproduction · 84

Monocytes are the primary carriers that transport Stx2 from the periphery to the kidney during STEC-induced HUS

peripheral thp-1 cfse-labeled evs single-cell flow toxin-cell
Tags for labeling protein N-termini with subtiligase for proteomics.

PMID 18762420 · PMC2590642 · Bioorganic & medicinal chemistry letters · 2008 · 6 claims · 4 setups

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Arginine-rich peptide esters (3, 4, 5) are markedly more soluble than the original TEVest2 ester (1) and give significantly higher N-terminal tagging of proteins by subtiligase at higher concentrations.

jurkat neutravidin-coated synthetic proteomic sds-page sandwich aqueous
Three assays show differences in binding of wild-type and mutant p53 to unique gene sequences.

PMID 19925028 · PMC2917581 · Technology in cancer research & treatment · 2009 · 7 claims · 6 setups

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Three different DNA binding assays (EMSA, SPA, streptavidin magnetic bead assay) show differences in binding of wild-type and mutant p53 to unique gene sequences

nuclear wro electrophoretic binding streptavidin
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

falciparum coli native falciparum-infected rt-pcr recombinant peptide

Experiments

The Proteomic Code: a molecular recognition code for proteins.

Autoantibody profiling for the study and treatment of autoimmune disease.

Stable isotope labeling tandem mass spectrometry (SILT): integration with peptide identification and extension to data-dependent scans.

Next-generation high-density self-assembling functional protein arrays.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

Pharmaco-proteomic study of hydroxyurea-induced modifications in the sickle red blood cell membrane proteome.

Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter.

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

Applying proteomics to the diagnosis and treatment of ALS and related diseases.

Monocytes serve as Shiga toxin carriers during the development of hemolytic uremic syndrome.

Tags for labeling protein N-termini with subtiligase for proteomics.

Three assays show differences in binding of wild-type and mutant p53 to unique gene sequences.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.