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).

• 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

• Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.

  PMID 16872520 · PMC1553449 · BMC genomics · 2006 · 8 claims · 7 setups

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  Native Peruvian H. pylori strains comprise two lineages: predominant hp-Europe and ~20% hsp-Amerind (Amerindian ancestry, closer to Alaska strains)

  pylori peruvian spanish fluorescent multilocus oipa

• High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

  PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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  WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

  genomic whole-genome same call snp technical genotype

• Relationship between cyclooxygenase 8473T>C polymorphism and the risk of lung cancer: a case-control study.

  PMID 16542464 · PMC1468421 · BMC cancer · 2006 · 8 claims · 4 setups

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  The COX-2 8473T>C genotype distribution did not differ significantly between overall lung cancer cases and controls.

  peripheral selected lung pcr-based sequencing questionnaire-based

• A common haplotype within the PON1 promoter region is associated with sporadic ALS.

  PMID 18618303 · PMC2739087 · Amyotrophic lateral sclerosis : official publication of the World Federation of Neurology Research Group on Motor Neuron Diseases · 2008 · 7 claims · 6 setups

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  Two SNPs (rs987539 in PON2 intron 6 and rs2074351 upstream of PON1 exon 2) within the paraoxonase gene cluster are significantly associated with susceptibility to sporadic ALS

  genomic case-control sporadic serum snp allelic sliding-window

• Two previously proposed P1/P2-differentiating and nine novel polymorphisms at the A4GALT (Pk) locus do not correlate with the presence of the P1 blood group antigen.

  PMID 16212661 · PMC1282566 · BMC genetics · 2005 · 8 claims · 4 setups

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  The previously proposed P2-specific markers -551_-550insC and -160A>G do not correlate with P1/P2 phenotype, since they occur homozygously in many P1 individuals too

  genomic erythrocytes direct pcr pcr-asp

• 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

• Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

  PMID 20021669 · PMC2803178 · BMC genetics · 2009 · 8 claims · 8 setups

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  WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays

  wga non-amplified archived serum-derived snp purification whole-genome

• Epithelial ovarian cancer: influence of polymorphism at the glutathione S-transferase GSTM1 and GSTT1 loci on p53 expression.

  PMID 8956789 · PMC2077203 · British journal of cancer · 1996 · 8 claims · 4 setups

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  GSTM1, GSTT1 and CYP2D6 genotype/allele frequencies did not differ significantly between 84 ovarian cancer cases and 325 controls, showing no association with disease susceptibility.

  leucocyte paraffin-embedded tumour pcr-amplified pcr-based immunohistochemistry single-strand

• Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection.

  PMID 16102740 · PMC7124242 · Clinica chimica acta; international journal of clinical chemistry · 2006 · 6 claims · 7 setups

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  The Luminex xMAP system uses spectrally distinct dyed microspheres (up to 100 sets) read by dual lasers to enable simultaneous multiplexed analysis of up to 100 reactions in one vessel.

  genomic apoe hla whole-genome direct oligonucleotide single

• Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

  PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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  HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

  genomic genotype 293t pcr-amplified pcr haplotype cell-cell

• Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies.

  PMID 16899448 · PMC1557808 · Nucleic acids research · 2006 · 7 claims · 4 setups

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  3D VizStruct (DFT-based radial mapping + KLD as z-axis) can identify SNPs/polymorphic markers that are predictive of underlying biological class distinctions across diverse datasets

  lpl y-chromosome coral simulated snp aflp numerical

• Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

  PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

  Has reproduction · 64

  L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

  elegans small small sequencing lifespan

• Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

  PMID 16981987 · PMC1592085 · BMC medical genetics · 2006 · 8 claims · 6 setups

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  Mutations were identified in 64 of 84 (76%) TSC probands, comprising 9 TSC1 and 55 TSC2 mutations

  genomic pcr-amplified tsc healthy dhplc direct pcr

• Molecular and immunohistochemical analysis of P53 in phaeochromocytoma.

  PMID 7577469 · PMC2033918 · British journal of cancer · 1995 · 6 claims · 4 setups

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  No p53 mutations were found in the hotspot region (exons 4-8) of 25 phaeochromocytomas by PCR-SSCP and sequencing

  phaeochromocytoma pcr-amplified formalin-fixed single pcr-sscp restriction immunohistochemistry

• Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study.

  PMID 16672055 · PMC1468397 · BMC medical genetics · 2006 · 6 claims · 5 setups

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  Molecular beacon-based real-time PCR assays for p.C282Y and p.H63D achieve complete genotype concordance with restriction enzyme digestion and direct sequencing

  genomic anonymized dried pcr-restriction direct molecular

• 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

• High-density SNP genotyping to define beta-globin locus haplotypes.

  PMID 18829352 · PMC4251776 · Blood cells, molecules & diseases · 2009 · 8 claims · 5 setups

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  RFLP analysis lacks sufficient site density/coverage to accurately reflect the genomic complexity of the β-locus

  genomic rflp subset rflp high-density haploview

• 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

• Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

  PMID 20042177 · PMC3026437 · American journal of ophthalmology · 2010 · 6 claims · 4 setups

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  The Gln192Arg PON1 polymorphism is associated with decreased susceptibility to AMD, particularly wet AMD, indicating a protective effect

  genomic pcr-amplified case-control pon1 single-strand direct genetic