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 180

System / cell line: probe ✕ Clear

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

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A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

genomic same synthetic invader pyrosequencing hplc
Statistical challenges in preprocessing in microarray experiments in cancer.

PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

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Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

lung beer individual outlier expression rank-covariance quality-control
Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
Phagosome maturation: going through the acid test.

PMID 18813294 · PMC2908392 · Nature reviews. Molecular cell biology · 2008 · 8 claims · 8 setups

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Maturation of apoptotic cell-containing phagosomes proceeds via machinery mechanistically distinct from receptor-mediated endocytosis

caenorhabditis elegans swiss phagosomes rnai genetic acridine
Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

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About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

genomic japanese reference snp concentration agarose
Five recurrent BRCA1/2 mutations are responsible for cancer predisposition in the majority of Slovenian breast cancer families.

PMID 18783588 · PMC2547096 · BMC medical genetics · 2008 · 8 claims · 5 setups

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Five recurrent mutations (1806C>T, 300T>G, 300T>A, 5382insC in BRCA1; IVS16-2A>G in BRCA2) are responsible for the majority of BRCA1/2-positive Slovenian families

leucocyte slovenian truncation denaturing multiplex
Ethnically diverse causes of Walker-Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East.

PMID 18752264 · PMC2577713 · Human mutation · 2008 · 8 claims · 4 setups

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40% (16/40) of WWS families in this diverse cohort received a molecular diagnosis with mutations in POMT1, POMT2, FKRP or FCMD

genomic pomt2 population genome-wide pcr multiplex
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
Autosomal dominant hereditary spastic paraplegia: novel mutations in the REEP1 gene (SPG31).

PMID 18644145 · PMC2492855 · BMC medical genetics · 2008 · 8 claims · 6 setups

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Pathogenic REEP1 mutations were identified in 4.3% (7/162) of autosomal dominant 'pure' HSP cases

genomic pcr-amplified reep1 pcr dhplc direct
A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

PMID 18518950 · PMC2464610 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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A new method for building reference gene-expression profiles and scoring/testing connections improves on the original Connectivity Map by enabling statistical significance testing of connections.

lines random gene-expression connectivity
Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

PMID 18489799 · PMC2413254 · BMC cancer · 2008 · 8 claims · 6 setups

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Pathogenic BRCA1/BRCA2 mutations were identified in 294 of 1,010 (29.1%) unrelated high-risk Czech probands

genomic pcr-amplified brca1 pha-stimulated truncation heteroduplex direct
Clinical characterization and the mutation spectrum in Swedish adenomatous polyposis families.

PMID 18433509 · PMC2386495 · BMC medicine · 2008 · 8 claims · 8 setups

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A combination of mutation-screening techniques (PTT, SSCP/HD, D-HPLC, sequencing, MLPA, mosaicism analysis, expression analysis) achieved a 100% mutation detection frequency in classical FAP

peripheral genomic cdna truncation sscp d-hplc
Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.

PMID 18276640 · PMC2346606 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Illumina HumanHap300 arrays are substantially more efficient than Affymetrix Genechip HindIII arrays for DNA-pooling based GWAS

pools same publicly simulated pooling individual simulation
Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments.

PMID 20043151 · PMC2825322 · Applied microbiology and biotechnology · 2010 · 8 claims · 8 setups

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Aerobic biodegradation of branched NP in polluted river sediment occurs within 8 days after a 2-day lag phase at 30°C

np-polluted sediment-derived fourth-generation extracted biodegradation serial metabolite
A small-cell lung cancer genome with complex signatures of tobacco exposure.

PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

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22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

nci-h209 sclc lu-135 massively pcr multiplex
Targeted disruption of the S1P2 sphingosine 1-phosphate receptor gene leads to diffuse large B-cell lymphoma formation.

PMID 19903857 · PMC2973841 · Cancer research · 2009 · 8 claims · 8 setups

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S1P2−/− mice develop clonal B-cell lymphomas with age, with ~half affected by 1.5-2 years

s1p2− lymphoma bone genomic necropsy histology flow
High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups

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Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature

yoruba selected subset whole-genome targeted pcr
A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

duke nci-60 mayo spanish gene cdna igvh
High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

universal same lim erythrocyte genome-wide cross-platform rt-pcr
A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

serum plasmids coli pcr oligonucleotide chip

Experiments

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

Statistical challenges in preprocessing in microarray experiments in cancer.

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

Phagosome maturation: going through the acid test.

Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

Five recurrent BRCA1/2 mutations are responsible for cancer predisposition in the majority of Slovenian breast cancer families.

Ethnically diverse causes of Walker-Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East.

Analysis of copy number variation using quantitative interspecies competitive PCR.

Autosomal dominant hereditary spastic paraplegia: novel mutations in the REEP1 gene (SPG31).

A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

Clinical characterization and the mutation spectrum in Swedish adenomatous polyposis families.

Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.

Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments.

A small-cell lung cancer genome with complex signatures of tobacco exposure.

Targeted disruption of the S1P2 sphingosine 1-phosphate receptor gene leads to diffuse large B-cell lymphoma formation.

High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.