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 15

System / cell line: allele ✕ Assay: pyrosequencing ✕ Clear

An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups

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An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.

lung hpl1d rrna external pcr rt-pcr quantitative
A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

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Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

falciparum cloned pyrosequencing pcr
Weak or no association of TCF7L2 variants with Type 2 diabetes risk in an Arab population.

PMID 18655717 · PMC2515290 · BMC medical genetics · 2008 · 8 claims · 4 setups

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rs7903146 T allele frequency does not differ significantly between Saudi T2D cases and controls (OR 1.04, 95% CI 0.86-1.27, P=0.675)

peripheral saudi genotype subset snp case-control haplotype
High-resolution, high-throughput HLA genotyping by next-generation sequencing.

PMID 19845894 · PMC4205125 · Tissue antigens · 2009 · 7 claims · 5 setups

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Clonal 454 sequencing reads (>250 nt) are long enough to span HLA exons and set phase of linked polymorphisms, resolving ambiguities inherent to Sanger-based heterozygote sequencing.

cell-line mixtures blood genomic flx amplicon pcr
A potentially deleterious new CYP2C9 polymorphism identified in an African American patient with major hemorrhage on warfarin therapy.

PMID 19083245 · PMC2662477 · Blood cells, molecules & diseases · 2009 · 7 claims · 4 setups

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A new CYP2C9 coding polymorphism, G1078A (D360N) in exon 7, was identified in an African American patient who experienced major gastrointestinal hemorrhage on warfarin therapy

african index cyp2c9 study pyrosequencing pcr custom
Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

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Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex
Competitive enzymatic reaction to control allele-specific extensions.

PMID 15767273 · PMC1065263 · Nucleic acids research · 2005 · 6 claims · 7 setups

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Protease-mediated allele-specific extension (PrASE) uses competition between polymerase activity and Proteinase K-mediated polymerase degradation to allow extension of perfectly matched primers while eliminating slower mismatched primer extension.

genomic immobilized four individuals multiplex protease-mediated effect
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
Resequencing of genes for transforming growth factor beta1 (TGFB1) type 1 and 2 receptors (TGFBR1, TGFBR2), and association analysis of variants with diabetic nephropathy.

PMID 17319955 · PMC1808054 · BMC medical genetics · 2007 · 7 claims · 7 setups

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TGFβ1 is a crucial mediator in the pathogenesis of diabetic nephropathy, promoting renal hypertrophy and extracellular matrix accumulation.

genomic healthy irish case mutation direct taqman
Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

PMID 18842779 · PMC3014055 · The American journal of clinical nutrition · 2008 · 8 claims · 4 setups

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A significant gene x diet interaction exists between 5-LO promoter short alleles (3,4 repeats) and dietary AA intake in determining MI risk

costa buffy genetic real-time allele-specific
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct
JAK2 V617F: a single mutation in the myeloproliferative group of disorders.

PMID 16755940 · PMC1891745 · The Ulster medical journal · 2006 · 8 claims · 8 setups

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A single acquired JAK2 mutation (V617F, G1849T in exon 14) is found across polycythaemia vera, essential thrombocythaemia and idiopathic myelofibrosis

blood haematopoietic granulocytes mpd pcr-direct sirna microsatellite
Genomic diversity of oseltamivir-resistant influenza virus A (H1N1), Luxembourg, 2007-08.

PMID 19788831 · PMC2819849 · Emerging infectious diseases · 2009 · 8 claims · 5 setups

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NA gene sequences of oseltamivir-resistant viruses (ORVs) form a distinct phylogenetic cluster separate from oseltamivir-sensitive viruses (OSVs)

influenza clinical partial sanger pyrosequencing molecular
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp
Concurrent genotyping of Helicobacter pylori virulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA.

PMID 18842150 · PMC2577186 · BMC microbiology · 2008 · 7 claims · 8 setups

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MDA-amplified DNA from minute gastric biopsy specimens enables concurrent PCR-based genotyping of bacterial (H. pylori) and human host genes from a single DNA source

mda-amplified pylori-positive multiplex pyrosequencing pcr

Experiments

An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

Weak or no association of TCF7L2 variants with Type 2 diabetes risk in an Arab population.

High-resolution, high-throughput HLA genotyping by next-generation sequencing.

A potentially deleterious new CYP2C9 polymorphism identified in an African American patient with major hemorrhage on warfarin therapy.

Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

Competitive enzymatic reaction to control allele-specific extensions.

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

Resequencing of genes for transforming growth factor beta1 (TGFB1) type 1 and 2 receptors (TGFBR1, TGFBR2), and association analysis of variants with diabetic nephropathy.

Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

JAK2 V617F: a single mutation in the myeloproliferative group of disorders.

Genomic diversity of oseltamivir-resistant influenza virus A (H1N1), Luxembourg, 2007-08.

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

Concurrent genotyping of Helicobacter pylori virulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA.