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 20

System / cell line: pre ✕ Assay: gel ✕ Clear

A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease.

PMID 19656391 · PMC2729079 · BMC cancer · 2009 · 8 claims · 4 setups

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2D gel proteomic profiling of immunodepleted serum reveals protein spot patterns that differentiate pre-cirrhotic NAFLD, cirrhotic NAFLD, and cirrhotic NAFLD with HCC

immunodepleted serum liver gel direct semi-quantitative
Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass.

PMID 18824761 · PMC2629397 · Circulation · 2008 · 8 claims · 3 setups

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CP/CPB causes multiple consistent, reproducible changes in the human myocardial (right atrial) protein profile

right excised 2-dimensional tandem sds-page
High-accuracy proteome maps of human body fluids.

PMID 17140426 · PMC1794581 · Genome biology · 2006 · 8 claims · 5 setups

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Large-scale, high-accuracy MS analyses of tear fluid, urine, and seminal plasma provide high-quality datasets useful for biomarker discovery

tear-duct urine seminal blood lc-ms large-scale decoy
Characterization of detergent-insoluble proteins in ALS indicates a causal link between nitrative stress and aggregation in pathogenesis.

PMID 19956584 · PMC2780298 · PloS one · 2009 · 8 claims · 8 setups

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The Triton X-100-insoluble fraction (TIF) from spinal cord of G93A SOD1 mice is enriched in specific proteins (cytoskeletal, chaperone, mitochondrial, metabolic, signaling) compared to WT mice, already at a preclinical stage.

spinal tif lumbar ventral gel maldi-tof western
Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer.

PMID 15199385 · PMC2364749 · British journal of cancer · 2004 · 7 claims · 7 setups

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Six serum protein spots (~40 kDa, pI 5.9–6.6) significantly overexpressed in grade 1, 2 and 3 ovarian cancer patients were identified by MALDI-TOFMS and n-ESIQ(q)TOFMS as isoforms of haptoglobin-1 precursor (HAP1)

serum tryptic 2de-separated paraffin-embedded two-dimensional affi-gel maldi-tofms
CyDye immunoblotting for proteomics: co-detection of specific immunoreactive and total protein profiles.

PMID 17111436 · PMC2978322 · Proteomics · 2006 · 7 claims · 4 setups

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CyDye immunoblotting (ECL Plex) allows simultaneous co-detection of total protein profile and a specific immunoreactive protein on the same membrane

left tryptic 1-d 2-de maldi-tof
Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.

PMID 17537823 · PMC1919476 · Nucleic acids research · 2007 · 6 claims · 8 setups

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Endogenous nuclear pre-mRNA processing complexes (supraspliceosomes) were purified at preparative scale from human HeLa cells and chicken DT40 pre-B cells for compositional analysis

hela chicken supraspliceosome extracts glycerol tandem mass
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

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Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

gria2 drosophila nova1 cd45 splicing sirna hits-clip
Preclinical and post-treatment changes in the HCC-associated serum proteome.

PMID 17060939 · PMC2360589 · British journal of cancer · 2006 · 7 claims · 6 setups

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SELDI proteomic profiling of serum reveals consistent, statistically significant changes associated with the development of HCC in hepatitis C patients

serum pooled excised seldi-tof anion lc-ms
Dissociation of the carbohydrate-binding and splicing activities of galectin-1.

PMID 18662664 · PMC2590671 · Archives of biochemistry and biophysics · 2008 · 7 claims · 7 setups

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GST-Gal3 and GST-Gal1 pull down the general transcription factor TFII-I from HeLa nuclear extract, identified by mass spectrometry and confirmed by immunoblot

hela gst-gal1 galectin-depleted gst lc-ms immunoblotting
Heterogeneity of p53 mutational status in esophageal squamous cell carcinoma.

PMID 9617346 · PMC5921814 · Japanese journal of cancer research : Gann · 1998 · 6 claims · 4 setups

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Three of 10 esophageal squamous cell carcinomas showed heterogeneous p53 mutational status, but only within the pre-invasive (carcinoma in situ) area.

esophageal paraffin-embedded genomic biotinylated immunohistochemistry microdissection nested
Application of single molecule technology to rapidly map long DNA and study the conformation of stretched DNA.

PMID 16243782 · PMC1266062 · Nucleic acids research · 2005 · 7 claims · 4 setups

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DLA can generate a high signal-to-noise bisPNA binding-site map of the 185.1 kb BAC 12M9 using as few as 200 molecule traces

bac direct pulsed-field electrophoretic
The nuclear pore complex.

PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

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NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a
Genome amplification of single sperm using multiple displacement amplification.

PMID 15942023 · PMC1143700 · Nucleic acids research · 2005 · 8 claims · 7 setups

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MDA was applied for the first time to whole-genome amplification of single sperm cell DNA

single sperm pcr sanger real-time
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

PMID 20037647 · PMC2793016 · PloS one · 2009 · 7 claims · 7 setups

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A dirty genome approach using unfinished, unclosed genome sequences combined with proteomics can rapidly identify immunogenic proteins useful for diagnostic tool development

parachlamydia spots coli recombinant pyrosequencing solexa gel
Squamous morules are functionally inert elements of premalignant endometrial neoplasia.

PMID 19180120 · PMC2633489 · Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2009 · 8 claims · 5 setups

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Squamous morules are hormonally incompetent, lacking ER/PR expression and proliferative activity, unlike the glandular component

endometrial ein microdissected morule-bearing immunohistochemistry laser retrospective
Use of proteomics for validation of the isolation process of clotting factor IX from human plasma.

PMID 19819359 · PMC2818390 · Journal of proteomics · 2010 · 8 claims · 8 setups

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Proteomic techniques (LC-MS/MS, iTRAQ, immunochemical/biochemical methods) can monitor and validate each production step of pd F IX isolation

plasma in-process chromatographic one-stage competitive elisa
Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.

PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups

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Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain

frontal excised synaptosome paraffin-embedded 2d-page maldi-tof western
Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa.

PMID 19656662 · PMC2744841 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

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Pyrosequencing™ can substitute for traditional sequencing methods, providing rapid (<1 h) and reliable detection of antibiotic resistance mutations in P. aeruginosa

clinical extracted pcr fluoroquinolone-resistant kirby–bauer multiplex sanger
Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

porcine paec umbilical huvec methyltransferase sds-page fragmentation

Experiments

A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease.

Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass.

High-accuracy proteome maps of human body fluids.

Characterization of detergent-insoluble proteins in ALS indicates a causal link between nitrative stress and aggregation in pathogenesis.

Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer.

CyDye immunoblotting for proteomics: co-detection of specific immunoreactive and total protein profiles.

Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

Preclinical and post-treatment changes in the HCC-associated serum proteome.

Dissociation of the carbohydrate-binding and splicing activities of galectin-1.

Heterogeneity of p53 mutational status in esophageal squamous cell carcinoma.

Application of single molecule technology to rapidly map long DNA and study the conformation of stretched DNA.

The nuclear pore complex.

Genome amplification of single sperm using multiple displacement amplification.

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

Squamous morules are functionally inert elements of premalignant endometrial neoplasia.

Use of proteomics for validation of the isolation process of clotting factor IX from human plasma.

Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.

Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa.

Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.