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 108

Assay: fractionation ✕ Clear

Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

Has reproduction · 90

MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent
Brown fat activation reduces hypercholesterolaemia and protects from atherosclerosis development.

PMID 25754609 · PMC4366535 · Nature communications · 2015 · 7 claims · 8 setups

Has reproduction

β3-AR agonist-mediated BAT activation reduces plasma triglycerides and cholesterol and protects against atherosclerosis development in APOE*3-Leiden.CETP mice.

e3l.cetp interscapular liver aortic indirect histology plasma
Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation.

PMID 34795257 · PMC8602323 · Nature communications · 2021 · 8 claims · 12 setups

Has reproduction · 67

PYK2 was identified as a putative IRF5 kinase via a kinase inhibitor library screen in macrophages

raw264.7 hektlr4 hoxb8-derived colon kinase co-immunoprecipitation co-ip
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 100

TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

hesc hescs long-read short-read rt-pcr
High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy.

PMID 17184556 · PMC1797031 · Breast cancer research : BCR · 2006 · 8 claims · 8 setups

Full-text index only

Plasma is well suited to proteomic biomarker discovery because it is easily obtained, routinely used diagnostically, and has a rich proteome.

plasma serum maldi-tof seldi-tof tandem
Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

PMID 17486137 · PMC2673710 · Molecular systems biology · 2007 · 8 claims · 7 setups

Full-text index only

Global MudPIT-based proteomic profiling across six mouse lung developmental time points (E13.5–P56) identifies thousands of proteins and captures developmental/cell-biological expression patterns.

lung analysis embryonic homologues shotgun microarray k-nearest
Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

PMID 17446074 · PMC1885954 · Current biology : CB · 2007 · 8 claims · 8 setups

Full-text index only

Newly synthesized ribosomal proteins accumulate in nucleoli more quickly than other nucleolar proteins

hela post-mitotic pulsed fluorescence selective
Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.

PMID 19121650 · PMC2706936 · Journal of proteomics · 2009 · 7 claims · 5 setups

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A new MRM worksheet was implemented in The Global Proteome Machine database (GPMDB) that provides all information needed to design MRM transitions based solely on archived observations from previous experiments by other researchers.

platelet proteins reaction midas mrm
Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups

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Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.

blood schizophrenia sjl serum proteomic differential comparative
Metabolism as a complex genetic trait, a systems biology approach: implications for inborn errors of metabolism and clinical diseases.

PMID 18836848 · PMC4319114 · Journal of inherited metabolic disease · 2008 · 7 claims · 8 setups

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Synergistic heterozygosity — cumulative heterozygous mutations at multiple loci in functionally related metabolic pathways — can cause physiologically relevant reduction of pathway flux and disease.

models liver sucrose vlcad-deficient physiological blue sucrose
The proteogenomic path towards biomarker discovery.

PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

Full-text index only

Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

renal urine breast chronic microarray immunoassay gel
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

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High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

tuberculosis sanger spectra lc-ms sds-page signal
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
Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

PMID 19902006 · PMC2774473 · Journal of biomedicine & biotechnology · 2010 · 8 claims · 5 setups

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iTRAQ labelling combined with 4800 MALDI TOF/TOF can detect quantitative differences in the maternal plasma proteome between DS and euploid pregnancies

maternal tryptic scx-fractionated identified itraq immunodepletion strong
Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

PMID 19853919 · PMC2787966 · Molecular immunology · 2009 · 7 claims · 6 setups

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OAS2 is identified as a novel NOD2-binding partner in THP-1 cells by tandem affinity purification and mass spectrometry

thp-1 hek293 tandem co-immunoprecipitation oas2
Neuroscience in the era of functional genomics and systems biology.

PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

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Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

developing hippocampus bac-transgenic fetal situ gene bac-transgenic
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
Novel approaches for identifying target antigens of autoreactive human B and T cells.

PMID 19763575 · PMC2845891 · Seminars in immunopathology · 2009 · 8 claims · 8 setups

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CD8+ T cells infiltrating MS brain and IM muscle tissue show clonal expansions consistent with antigen-driven selection

muscle brain morphologically autopsy cdr3-spectratyping single-cell immunohistochemistry
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

Full-text index only

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
iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.

PMID 19674965 · PMC2773724 · Molecular & cellular proteomics : MCP · 2009 · 6 claims · 5 setups

Full-text index only

Serial transplantation of human GBM xenografts in nude rats converts an initially highly infiltrative, non-angiogenic phenotype into a highly angiogenic phenotype over 4-6 generations.

membrane-enriched xenograft homogenate quantified itraq western bradford

Experiments

Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

Brown fat activation reduces hypercholesterolaemia and protects from atherosclerosis development.

Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation.

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy.

Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.

Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

Metabolism as a complex genetic trait, a systems biology approach: implications for inborn errors of metabolism and clinical diseases.

The proteogenomic path towards biomarker discovery.

High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

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

Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

Neuroscience in the era of functional genomics and systems biology.

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

Novel approaches for identifying target antigens of autoreactive human B and T cells.

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

iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.