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).

• 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

• High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

  PMID 18344524 · PMC2367728 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  A protocol combining PCR-based whole genome amplification with arrays of highly purified BAC clones enables detection of DNA copy number changes in single cells

  single bac amplified pi-scei array quantitative dot

• 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

• High resolution array-CGH analysis of single cells.

  PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

  769p hct116 peripheral single array-cgh gel fish

• Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

  PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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  The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

  dog hamster pcr primer pcr blast sequence

• 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

• 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

• Whole genome amplification and de novo assembly of single bacterial cells.

  PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups

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  FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions

  prochlorococcus single-cell seven sag genome spike-in amplification

• BRCA1 mutations in southern England.

  PMID 9649133 · PMC2150412 · British journal of cancer · 1998 · 7 claims · 4 setups

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  Early age of onset combined with a strong family history is the most effective selection criterion for detecting BRCA1 mutations, more so than bilaterality alone

  genomic pcr clinical heteroduplex sequencing pcr

• Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil.

  PMID 10081673 · PMC2627691 · Emerging infectious diseases · 1999 · 8 claims · 8 setups

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  Among 79 HIV-1 infected patients, 3 (3.8%) had dual infections, 6 (7.6%) had recombinant infections, and 70 (88.6%) had single-subtype infections

  pbmc uncultured pcr-amplified aligned rflp heteroduplex nested

• Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

  PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups

  Has reproduction · 44

  Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.

  plasmid coli wild-type artificial smrt read-mixing distributional

• Mutation analysis of genes that control the G1/S cell cycle in melanoma: TP53, CDKN1A, CDKN2A, and CDKN2B.

  PMID 15819981 · PMC1097717 · BMC cancer · 2005 · 7 claims · 4 setups

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  TP53 gene shows heterozygous defects in 8 of 39 (20.5%) melanoma tumors, including novel point mutations and novel SNPs in intronic sequences

  metastatic melanoma genomic pcr-sscp sequencing pcr

• Multiplex SNaPshot for detection of BRCA1/2 common mutations in Spanish and Spanish related breast/ovarian cancer families.

  PMID 17603881 · PMC1924843 · BMC medical genetics · 2007 · 7 claims · 4 setups

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  Ten recurrent/founder mutations (5 in BRCA1, 5 in BRCA2, including the newly observed BRCA2 c.5374-5377delTATG) account for approximately 50% of BRCA1/2 mutations identified in Spanish families

  genomic same pcr multiplex pcr snapshot

• 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

• High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro.

  PMID 35776646 · PMC9243297 · STAR protocols · 2022 · 8 claims · 8 setups

  Has reproduction · 65

  HT-SELEX enables unbiased, in vitro determination of preferred DNA target motifs for DNA-binding proteins by iterative selection and PCR amplification of bound oligonucleotides

  synthetic pcr-generated selex histidine-tagged pcr polyacrylamide spectrophotometry

• Analysis of the p53 gene by PCR-SSCP in ten cases of Wilms' tumor.

  PMID 10772697 · PMC11166235 · Sao Paulo medical journal = Revista paulista de medicina · 2000 · 7 claims · 3 setups

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  Point mutations of the p53 gene (exons 5-9) were not detected in any of the 10 Wilms' tumor samples studied

  extracted pcr-amplified pcr pcr pcr-sscp automated

• A colorimetric method for point mutation detection using high-fidelity DNA ligase.

  PMID 16257979 · PMC1275593 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  High-fidelity Tth DNA ligase combined with allele-specific ligation-based gold nanoparticle assembly enables colorimetric single-base discrimination without precise temperature control

  p3-modified nanoparticle synthetic ligated uv-vis colorimetric melting

• Familial hypercholesterolemia in St-Petersburg: the known and novel mutations found in the low density lipoprotein receptor gene in Russia.

  PMID 15701167 · PMC551615 · BMC medical genetics · 2005 · 8 claims · 6 setups

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  21 rare sequence variations of the LDL receptor gene were identified in St.-Petersburg FH patients, 19 of which are probably pathogenic and 2 (P518P, T705I) neutral.

  genomic pcr proband restriction sscp automated

• HIT: a versatile proteomics platform for multianalyte phenotyping of cytokines, intracellular proteins and surface molecules.

  PMID 18849997 · PMC3334282 · Nature medicine · 2008 · 8 claims · 8 setups

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  HIT uses oligonucleotide-tagged (Fab- or mSA-conjugated) antibodies, T7 polymerase amplification, and DNA microarray hybridization to indirectly measure multiple analytes in a fluid-phase multiplex format

  hsp70-coated hsp70 secreted jurkat fluid-phase multiplex hit

• Novel mutations in the BRCA1 and BRCA2 genes in Iranian women with early-onset breast cancer.

  PMID 12100744 · PMC116720 · Breast cancer research : BCR · 2002 · 8 claims · 4 setups

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  Germline BRCA1 and BRCA2 mutations are present in Iranian women with early-onset breast cancer, including four novel frameshift mutations

  genomic pcr-amplified pcr truncation single-strand heteroduplex