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).
-
Full-text index only
Quantitative phosphoproteomics by mass spectrometry: past, present, and future.
PMID 18846511 · PMC2701620 · Proteomics · 2008 · 8 claims · 6 setups
Selective enrichment of phosphopeptides (antiphosphotyrosine IP, IMAC, TiO2/MOAC, SCX, chemical tagging) is required to detect substoichiometric, transient phosphorylation events by MS
-
Has reproduction · 80
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.
PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups
BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules
-
Has reproduction · 80
Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.
PMID 33999949 · PMC8158866 · PLoS pathogens · 2021 · 8 claims · 8 setups
MCPyV generates two circular RNAs (circALTO1, circALTO2) spanning the early region/ALTO ORF, detectable in VP-MCC cell lines and patient tumors
-
Full-text index only
An initial characterization of the serum phosphoproteome.
PMID 19824718 · PMC2789176 · Journal of proteome research · 2009 · 8 claims · 8 setups
A TiO2-based phosphopeptide enrichment method coupled with LC-MS/MS (LTQ-Orbitrap CID and LTQ-ETD) was developed and applied to characterize the serum phosphoproteome
-
Full-text index only
Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation.
PMID 18784923 · PMC2755762 · Annals of hematology · 2009 · 6 claims · 4 setups
A non-radioactive, enzyme-coupled luminometric assay can quantify Ras activation as %GTP/(GTP+GDP) with high sensitivity (detects 1 fmol GTP)
-
Has reproduction · 74
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups
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.
-
Full-text index only
A global proteomics approach identifies novel phosphorylated signaling proteins in GPVI-activated platelets: involvement of G6f, a novel platelet Grb2-binding membrane adapter.
PMID 16941570 · PMC1869047 · Proteomics · 2006 · 8 claims · 7 setups
96 proteins undergo post-translational modification (phosphorylation) in response to CRP stimulation of human platelets, including 11 proteins not previously identified in platelets
-
Has reproduction · 87
High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies.
PMID 34010620 · PMC8096189 · Cell · 2021 · 8 claims · 5 setups
A Phage-DMS library tiling all single amino acid mutations across the SARS-CoV-2 spike ectodomain (plus D614G) was generated and validated with high sequence coverage.
-
Full-text index only
Extent of laminin-5 assembly and secretion effect junctional epidermolysis bullosa phenotype.
PMID 9547338 · PMC2212220 · The Journal of experimental medicine · 1998 · 6 claims · 6 setups
The most severe (Herlitz) form of JEB correlates best with mutations causing premature termination codons (PTCs), not with mutation location in a particular protein domain
-
Full-text index only
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
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
-
Full-text index only
Identification of a dominant epitope of glutamic acid decarboxylase (GAD-65) recognized by autoantibodies in stiff-man syndrome.
PMID 8245784 · PMC2191306 · The Journal of experimental medicine · 1993 · 8 claims · 6 setups
All 30 SMS patient sera selectively recognize GAD-65, but not GAD-67, when tested by Western blotting on denatured GAD.
-
Full-text index only
The current state of proteomics in GI oncology.
PMID 19104933 · PMC3045515 · Digestive diseases and sciences · 2009 · 8 claims · 8 setups
More than 130 exploratory proteomic studies have defined candidate biomarkers in serum, GI fluids, or cancer tissue for GI oncology
-
Full-text index only
Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.
PMID 15686596 · PMC549029 · Molecular cancer · 2005 · 8 claims · 5 setups
A chromatin library coupled with experimental validation can productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.
-
Full-text index only
An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.
PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups
The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups
-
Full-text index only
Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy.
PMID 15987476 · PMC1175022 · Arthritis research & therapy · 2005 · 8 claims · 8 setups
SELDI-TOF MS can differentiate serum protein profiles of active versus well-controlled SJIA
-
Full-text index only
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.
PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups
A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning
-
Full-text index only
Functional effects of KCNE3 mutation and its role in the development of Brugada syndrome.
PMID 19122847 · PMC2585750 · Circulation. Arrhythmia and electrophysiology · 2008 · 7 claims · 5 setups
A missense R99H mutation in KCNE3 was identified in a Brugada Syndrome proband and cosegregates with the phenotype in the family (4/4 phenotype-positive, 0/3 phenotype-negative members carried it)
-
Full-text index only
A novel breast cancer-associated BRIP1 (FANCJ/BACH1) germ-line mutation impairs protein stability and function.
PMID 18628483 · PMC2561321 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 6 claims · 7 setups
A novel heterozygous BRIP1 germline mutation (c.2992-2995delAAGA) was identified in a breast cancer patient, causing a frameshift and premature stop codon in exon 20.
-
Full-text index only
Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.
PMID 19929607 · PMC2931417 · Expert review of proteomics · 2009 · 8 claims · 8 setups
Serine/threonine phosphorylation widely functions to modulate protein-protein interactions (PPIs) across signaling systems
-
Full-text index only
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
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.