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 270

Assay: fluorescence ✕ Clear

Interactome networks: the state of the science.

PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

genes tnfα orf proteins yeast tandem interference
Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

genomic maternal 22qtdr chromosome semi-quantitative pcr fish
Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

PMID 16319823 · PMC1477589 · European journal of human genetics : EJHG · 2006 · 7 claims · 8 setups

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ALX4 and MSX2 mutations contribute approximately equally to PFM/CB and cause skull defects that are usually clinically indistinguishable

pfm selected point-mutation-negative family dhplc bidirectional multiplex
Viroporin potential of the lentivirus lytic peptide (LLP) domains of the HIV-1 gp41 protein.

PMID 18028545 · PMC2211469 · Virology journal · 2007 · 8 claims · 4 setups

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Synthetic peptides corresponding to LLP-1, LLP-2, and LLP-3 domains partition into POPC:POPG lipid membranes and adopt amphipathic α-helical secondary structure

hiv-1 synthetic nbd 90%popc wimley-white circular tryptophan
TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

PMID 17526832 · PMC2884950 · Microbiology (Reading, England) · 2007 · 7 claims · 8 setups

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tccP2 is present in 26 of 27 (96.2%) EPEC 2 lineage strains and absent from all 34 EPEC 1 strains tested

clinical pcr-negative representative whole-cell conventional colony locus-specific
Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

PMID 17470268 · PMC1868757 · BMC genomics · 2007 · 8 claims · 7 setups

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graCNV uses re-annotated Affymetrix expression microarray probe sets and the WPP algorithm to measure DNA copy number variation at a median resolution of ~17,500 bp without genomic complexity reduction.

neuroblastoma same normal megabladder acgh bac principal
Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

PMID 17392682 · PMC2642915 · Molecular vision · 2007 · 8 claims · 8 setups

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MLF accumulation more closely reflects the onset of AMD than LF accumulation

donor arpe-19 mlf sucrose phototoxicity fluorescence
Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

PMID 17303479 · PMC7105233 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 5 claims · 5 setups

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Pre-fractionation of plasma with immuno-affinity depletion and anion-exchange chromatography prior to 2D-DIGE substantially increases the number of detectable protein spots compared with unfractionated plasma.

plasma excised fractionated 2d-dige multi-dimensional lc-ms
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

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Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

liver chimpanzee h-invitational tar genome blastn secondary
Differences in the histological findings, phenotypic marker expressions and genetic alterations between adenocarcinoma of the gastric cardia and distal stomach.

PMID 17262083 · PMC2360051 · British journal of cancer · 2007 · 8 claims · 6 setups

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C-Ca is associated with a significantly higher incidence of differentiated-type tumours and lymphatic vessel invasion (LVI) compared with D-Ca

resected c-ca microdissected formalin-fixed histopathological immunohistochemistry pcr-single-strand
Fucosylated glycoproteins as markers of liver disease.

PMID 19126969 · PMC3827789 · Disease markers · 2008 · 8 claims · 6 setups

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Core alpha 1,6-linked fucosylation of AFP (AFP-L3) is increased in HCC and is a more specific marker of HCC than total AFP

afp pooled larger igg lectin fucose-specific immunoblot
Proteomic identification of non-Gal antibody targets after pig-to-primate cardiac xenotransplantation.

PMID 18957049 · PMC2586876 · Xenotransplantation · 2008 · 8 claims · 6 setups

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Non-Gal antibody response after cardiac xenotransplantation is directed to a diverse set of stress response, inflammation-related, cytoskeletal and metabolic pig EC antigens, with several immunodominant targets remaining undefined

gt-ko spots explanted flow western nanolc
Human Proteinpedia: a unified discovery resource for proteomics research.

PMID 18948298 · PMC2686511 · Nucleic acids research · 2009 · 8 claims · 8 setups

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Human Proteinpedia is a community portal using a distributed annotation system (DAS) to share both published and unpublished human proteomic data

proteins tissues plasma expressing tandem immunohistochemistry mass
Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

PMID 18922787 · PMC3523710 · Science signaling · 2008 · 8 claims · 8 setups

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VILIP1 was identified via a proteomic (GST pull-down) approach as a protein interacting with the P2X2 receptor C-terminal tail

brain hek gst co-immunoprecipitation immunocytochemistry
Association of GSK3B with Alzheimer disease and frontotemporal dementia.

PMID 18852354 · PMC2841136 · Archives of neurology · 2008 · 8 claims · 5 setups

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The GSK3B intronic polymorphism IVS2-68G>A is associated with increased risk of AD and FTD in a case-control cohort

genomic case-control family-based sib-pair pcr allele-specific fluorescence-polarization
Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups

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GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage

pools pcr genomic gs-flx massively sanger pcr
Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

PMID 18832376 · PMC2577333 · Nucleic acids research · 2008 · 8 claims · 6 setups

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A novel enhancer trap method retrofitting BACs with Tn10-based transposons enables nontargeted, functional mapping of noncontiguous cis-regulatory elements as zebrafish transgenes.

zebrafish bac genomic transgenic field bac
Analysis of copy number variation using quantitative interspecies competitive PCR.

PMID 18697816 · PMC2553599 · Nucleic acids research · 2008 · 7 claims · 6 setups

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qicPCR uses the entire genome of a single chimpanzee as a competitor, requiring only one reference sample for all assays and enabling large-scale multiplexing

genomic single 22q11ds qicpcr-derived qicpcr mlpa fluorescence
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

Experiments

Interactome networks: the state of the science.

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

Viroporin potential of the lentivirus lytic peptide (LLP) domains of the HIV-1 gp41 protein.

TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

Differences in the histological findings, phenotypic marker expressions and genetic alterations between adenocarcinoma of the gastric cardia and distal stomach.

Fucosylated glycoproteins as markers of liver disease.

Proteomic identification of non-Gal antibody targets after pig-to-primate cardiac xenotransplantation.

Human Proteinpedia: a unified discovery resource for proteomics research.

Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

Association of GSK3B with Alzheimer disease and frontotemporal dementia.

Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

Analysis of copy number variation using quantitative interspecies competitive PCR.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.