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).

• V-MitoSNP: visualization of human mitochondrial SNPs.

  PMID 16907992 · PMC1564046 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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  V-MitoSNP integrates RFLP genotyping information with mitochondria-related cancer/disease data in a user-friendly, interactive, color-coded visual web interface

  blood blood-derived mtdna standard agarose rflp

• Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

  PMID 16670016 · PMC1513378 · Lipids in health and disease · 2006 · 8 claims · 6 setups

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  A -987C>T polymorphism located 4bp from the 3' end of the MseI RFLP forward primer causes allelic drop-out, producing incorrect -1131T>C genotypes.

  asian random subjects unrelated arms-pcr msei sanger

• Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

  PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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  Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

  large-insert patients test genomic array-cgh manual automated

• 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

• Genomic structure and alterations of homeobox gene CDX2 in colorectal carcinomas.

  PMID 10027310 · PMC2362430 · British journal of cancer · 1999 · 8 claims · 6 setups

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  CDX2 expression is decreased in colorectal carcinomas in prior studies

  genomic sporadic hnpcc carcinoma standard pcr-sscp cloning

• BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes.

  PMID 15653630 · PMC546182 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  BiSearch is a new web-available primer-design software for bisulfite-treated genomes that also analyzes primer pairs for mispriming sites via a novel search algorithm.

  tyrosine homo hek primer post-design pcr

• EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

  PMID 16381980 · PMC1347508 · Nucleic acids research · 2006 · 7 claims · 4 setups

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  EPD is an annotated, non-redundant collection of experimentally defined eukaryotic POL II promoters accessed via genome position pointers.

  rice preliminary primer sequence quality

• Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions.

  PMID 15958788 · PMC1150895 · Nucleic acids research · 2005 · 6 claims · 4 setups

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  SNaPshot primers with mismatches to upstream bisulfite-induced C/T or G/A polymorphisms produce a position-dependent biasing effect of up to 70%, decreasing as the mismatch moves farther upstream of the target cytosine

  comt synthetic genomic 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

• A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

  PMID 16351727 · PMC1327677 · BMC genomics · 2005 · 8 claims · 5 setups

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  A qPCR method using unique-sequence primers can reproducibly detect chromosomal microdeletions and microduplications

  genomic genome pcr real-time fluorescence sequence

• Deletion of the V2 vasopressin receptor gene in two Chinese patients with nephrogenic diabetes insipidus.

  PMID 17101063 · PMC1657029 · BMC genetics · 2006 · 7 claims · 6 setups

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  The two NDI patients carry a 5,995-bp genomic deletion combined with a 3-bp (GAG) insertion at Xq28 that removes the entire AVPR2 gene and the last exon (exon 22) of the C1 (ARHGAP4) gene.

  genomic proband blood patients pcr long-range combined

• Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

  PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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  UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

  liver caucasian ugt2b7 gene snp enzymatic

• BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).

  PMID 16439806 · PMC1356528 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  oaCGH, not BAC CGH arrays, is the platform that will prevail in the future

  genomic lung genetics bt474 array exon

• Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR.

  PMID 17439964 · PMC1888819 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Bisulfite treatment causes DNA strand breakage (via abasic site formation and beta-elimination) in addition to cytosine deamination.

  genomic synthetic bisulfite-treated cloned methylation-sensitive quantitative gel

• Database resources of the National Center for Biotechnology Information.

  PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

  genbank genomic eukaryotic completely sequence rapid est