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 24

System / cell line: products ✕ Assay: snp ✕ Clear

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
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

pcr candidate embl clinical snp manual homology
Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

PMID 18074030 · PMC2111048 · PloS one · 2007 · 8 claims · 7 setups

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MDA-based single-cell whole-genome amplification (S-WGA) products show large variability in amplification bias, including allele dropout and preferential amplification.

lymphoblastoid lcl cmk11-5 gel taqman oligonucleotide
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
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

genomic ecotilling non-synonymous ecotilling sanger universal-primer
Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

PMID 17587445 · PMC1913537 · BMC genetics · 2007 · 6 claims · 4 setups

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CCR7 gene variants occur at extremely low frequency (allelic frequencies ≤5%) in the German population

genomic hut78 t-cells direct pcr dual
Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

PMID 18036257 · PMC2222243 · BMC medical genetics · 2007 · 8 claims · 5 setups

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Resequencing 81 candidate osteoporosis genes in 24 Koreans identified 942 variants (888 SNPs, 43 indels, 11 microsatellites)

genomic sequenced korean common sanger sequence population
A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction.

PMID 19956411 · PMC2786888 · Molecular vision · 2009 · 6 claims · 7 setups

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A novel de novo heterozygous nonsense mutation (c.413C>G, p.S138X) in OTX2 causes an early onset retinal dystrophy accompanied by pituitary dysfunction (growth hormone deficiency)

genomic anonymous single direct lca mismatch
Predicting failure rate of PCR in large genomes.

PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

genomic genome pcr combined large-scale exact-match mismatch-tolerant
Genome amplification of single sperm using multiple displacement amplification.

PMID 15942023 · PMC1143700 · Nucleic acids research · 2005 · 8 claims · 7 setups

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MDA was applied for the first time to whole-genome amplification of single sperm cell DNA

single sperm pcr sanger real-time
Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.

PMID 18664269 · PMC2515158 · BMC microbiology · 2008 · 8 claims · 7 setups

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18 STR loci (1-5 base repeat units, copy number 4-26) were identified in the M. genitalium G37 genome via bioinformatics analysis.

genitalium clinical selected 246-bp bioinformatics pcr plasmid
Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons.

PMID 18448472 · PMC2425497 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Internal oligonucleotide calibration improves homozygote genotyping accuracy for base-pair neutral small amplicons from 91.7% to 99.7% across five of six targets

genomic high-resolution sanger probe-based
Minisequencing mitochondrial DNA pathogenic mutations.

PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

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A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

blood-derived same genomic pcr minisequencing automatic multiplex
Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population.

PMID 19723304 · PMC2748065 · BMC medical genetics · 2009 · 7 claims · 4 setups

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Three NOD1 Exon 6 SNPs (W219R, L349P, L370R) show statistically significant association with ulcerative colitis compared to controls

genomic pcr patients dhplc cloning pcr-rflp
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

PMID 16336695 · PMC1325232 · Respiratory research · 2005 · 6 claims · 8 setups

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There is overall little sequence variation in the conserved non-coding elements (CNEs) on 5q31, including none detected in CNE-B/CNS-1

genomic pcr large outbred comparative denaturing pcr
Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

PMID 20011630 · PMC2790479 · Molecular vision · 2009 · 8 claims · 5 setups

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MDH1 is not the causative gene for RP28-linked autosomal recessive retinitis pigmentosa

genomic lr-pcr uhts v-4 long-range ultra sanger
Exome sequencing of a multigenerational human pedigree.

PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

genomic eluted captured pcr microarray-based qpcr next-generation
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

tumors cancer tumor lung direct database quantitative
Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.

PMID 17088437 · PMC2705832 · Molecular cancer therapeutics · 2006 · 8 claims · 3 setups

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137 oncogenic mutations were identified across 14 of 24 screened cancer genes (APC, BRAF, CDKN2A, CTNNB1, HRAS, KRAS, NRAS, SMAD4, PIK3CA, PTEN, RB1, STK11, TP53, VHL) in the NCI-60 panel

nci-60 pcr multiplex snp
Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

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The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

cloned clinical hominis pcr culture sanger

Experiments

Competitive enzymatic reaction to control allele-specific extensions.

Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

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

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction.

Predicting failure rate of PCR in large genomes.

Genome amplification of single sperm using multiple displacement amplification.

Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.

Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons.

Minisequencing mitochondrial DNA pathogenic mutations.

Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population.

Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

Exome sequencing of a multigenerational human pedigree.

Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.

Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.