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).

• Shotgun haplotyping: a novel method for surveying allelic sequence variation.

  PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

  genomic long pcr ampicillin-resistant long cloning short

• Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Anglian Breast Cancer Study Group.

  PMID 11044354 · PMC2408797 · British journal of cancer · 2000 · 6 claims · 4 setups

  Full-text index only

  BRCA1 and BRCA2 mutations are rare in the general population and account for only a small fraction of all breast cancer in the UK

  genomic pedigrees first-degree study pcr pedigree-based age

• Predicting failure rate of PCR in large genomes.

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

  Full-text index only

  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

• Ovarian cancer has frequent loss of heterozygosity at chromosome 12p12.3-13.1 (region of TEL and Kip1 loci) and chromosome 12q23-ter: evidence for two new tumour-suppressor genes.

  PMID 9155043 · PMC2228239 · British journal of cancer · 1997 · 8 claims · 4 setups

  Full-text index only

  Two commonly deleted regions on chromosome 12 were identified in ovarian cancer: 12p12.3-13.1 (6/23 samples) and 12q23-ter (7/23 samples)

  ovarian loh pcr-sscp multiplex

• Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

  PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

  Full-text index only

  Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

  peripheral mhc2ta pcr sanger bisulfite cpg

• 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

  Full-text index only

  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

• Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.

  PMID 17317684 · PMC1874629 · Nucleic acids research · 2007 · 7 claims · 7 setups

  Full-text index only

  Gene-Collector is a method for multiplex nucleic acid amplification that specifically circularizes only correctly paired (cognate) PCR primer products on a Collector probe, degrading non-cognate artifacts by exonuclease treatment.

  genomic multiplex circularized circular multiplex probe-guided exonuclease

• Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

  PMID 11308259 · PMC2363857 · British journal of cancer · 2001 · 8 claims · 8 setups

  Full-text index only

  Two forms of SYT mRNA, N-SYT and a novel form I-SYT, are co-expressed in normal human tissues and in synovial sarcomas

  synovial ss-derived normal liver rt-pcr cloning densitometric

• Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

  PMID 15534692 · PMC526178 · PLoS biology · 2004 · 8 claims · 6 setups

  Full-text index only

  Intramolecular pairs of oppositely oriented Alu elements within the same pre-mRNA form dsRNA foldback structures that are major substrates for A-to-I RNA editing

  huge brain pre-mrna greater genomic rt-pcr quantitative

• Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

  PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

  Full-text index only

  Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold

  simulated real chromosome randomly simulation multiplex coverage-vs-n

• Microdroplet-based PCR enrichment for large-scale targeted sequencing.

  PMID 19881494 · PMC2779736 · Nature biotechnology · 2009 · 7 claims · 5 setups

  Full-text index only

  Microdroplet PCR enables massively parallel singleplex amplification (up to ~1.5 million reactions, up to 4,000 targets) for targeted sequencing enrichment

  genomic single targeted scale-up variant

• Mutational analyses of multiple target genes in histologically heterogeneous gastric cancer with microsatellite instability.

  PMID 10081489 · PMC5921733 · Japanese journal of cancer research : Gann · 1998 · 7 claims · 5 setups

  Full-text index only

  MSI frequency in gastric cancers with histological heterogeneity was 35% (7/20 cases) and 28% (11/40 tumor DNAs), consistent with prior gastric cancer MSI studies.

  formalin-fixed msi-positive surgically microsatellite pcr-sscp histopathological

• Mutations of the beta- and gamma-catenin genes are uncommon in human lung, breast, kidney, cervical and ovarian carcinomas.

  PMID 11437403 · PMC2363927 · British journal of cancer · 2001 · 7 claims · 4 setups

  Full-text index only

  β-catenin and γ-catenin gene mutations are uncommon in human lung, breast, kidney, cervical and ovarian carcinomas

  lung carcinoma lines pcr-sscp rt-pcr-sscp direct

• Quasimonomorphic mononucleotide repeats for high-level microsatellite instability analysis.

  PMID 15528790 · PMC3888729 · Disease markers · 2004 · 8 claims · 8 setups

  Full-text index only

  Mononucleotide repeats are more sensitive, specific, and easier to use than dinucleotide repeats for detecting MSI-H tumors

  msi-h colon hmsh6-mutated tumors pentaplex pcr dinucleotide

• Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

  PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

  Full-text index only

  QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

  paired colorectal genome normal quma auma bioinformatic

• Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

  PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups

  Full-text index only

  DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue

  nsclc matched lung quantitative pcr genomic

• A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

  PMID 37247570 · PMC10878300 · Ticks and tick-borne diseases · 2023 · 7 claims · 3 setups

  Full-text index only

  The MPAS pipeline is a portable, reproducible Nextflow-based bioinformatics pipeline that identifies and summarizes amplicon sequences produced by the MPAS assay.

  host-seeking mpas same targeted mpas clc

• The matrix metalloproteinase-3 (MMP-3) 5A/6A promoter polymorphism is not associated with ischaemic heart disease: analysis employing a family based approach.

  PMID 15665388 · PMC3839324 · Disease markers · 2004 · 6 claims · 3 setups

  Full-text index only

  The MMP-3 -1612 5A/6A polymorphism is not associated with ischaemic heart disease in an Irish population.

  peripheral family extended pcr-rflp combined pedigree

• TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

  PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 69

  TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.

  ppm1d-transgenic genome genome read touchdown-pcr

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

  Full-text index only

  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative