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 20

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

Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans.

PMID 19046425 · PMC2625370 · BMC genomics · 2008 · 6 claims · 7 setups

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Identified a 12-bp Bacteroidetes DNA barcode and a 26-bp degenerate Firmicutes DNA barcode within the 16S rRNA gene

16s brain cystic caecal barcode 16s metagenome
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
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
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

PMID 20037647 · PMC2793016 · PloS one · 2009 · 7 claims · 7 setups

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A dirty genome approach using unfinished, unclosed genome sequences combined with proteomics can rapidly identify immunogenic proteins useful for diagnostic tool development

parachlamydia spots coli recombinant pyrosequencing solexa gel
Massively parallel pyrosequencing in HIV research.

PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

mammoth hiv hiv-infected honey pyrosequencing pcr 16s
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
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
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

monocytogenes additional food j774 whole-genome comparative pcr
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
SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

PMID 15980532 · PMC1160243 · Nucleic acids research · 2005 · 7 claims · 3 setups

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SOP 3 v2 is a web-based application that outputs recommended forward/reverse PCR primers plus a sequencing primer optimized for sequence-based genotyping of human and mouse polymorphisms

genomic ncbi laboratory primer genomic
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
Genomic mutation rates: what high-throughput methods can tell us.

PMID 19644920 · PMC2952423 · BioEssays : news and reviews in molecular, cellular and developmental biology · 2009 · 8 claims · 8 setups

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High-throughput DNA analyses yield genome mutation rate estimates markedly higher than those obtained with pre-genomic strategies

cerevisiae elegans melanogaster mammals fluctuation mutation indirect
Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

pcr-amplified same sequence luciferase bioluminometric bati comparison
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
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
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
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

PMID 17105657 · PMC1657037 · BMC bioinformatics · 2006 · 6 claims · 5 setups

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PathogenMIPer designs unique, target-specific MIP probes, assembling all probe components (target-specific sequences, barcodes, universal primers, restriction sites) into ready-to-order probes for any genome.

hpv clinical biotinylated pcr mip molecular microarray
MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

PMID 18154640 · PMC2233610 · BMC medical genetics · 2007 · 8 claims · 6 setups

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Chromosome 8p23.1 has previously been proposed as a nuclear modifier locus for A1555G-associated hearing loss phenotype

blood a1555g lymphoblastoid nuclear pcr-rflp direct rt-pcr
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
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

Experiments

Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans.

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

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

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

Massively parallel pyrosequencing in HIV research.

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

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

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

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

SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

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

Genomic mutation rates: what high-throughput methods can tell us.

Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

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

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

Competitive enzymatic reaction to control allele-specific extensions.

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

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.

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.