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).

• Visualization-based discovery and analysis of genomic aberrations in microarray data.

  PMID 15953389 · PMC1181623 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  ChARMView integrates dynamic visualization with automated statistical analysis (EM-based breakpoint detection, one-sample sign test, permutation mean test) to discover chromosomal aberrations from array CGH and gene expression data

  saccharomyces breast yeast array gene

• "Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

  PMID 18973698 · PMC2583995 · Journal of translational medicine · 2008 · 7 claims · 6 setups

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  An oligo-array platform can detect BRCA1 SNPs, insertions, and deletions of known and unknown variants, including in heterozygous conditions, with accuracy comparable to direct sequencing

  genomic pcr mcf-10a brca1 oligo-nucleotide direct pcr

• Probing the cancer genome.

  PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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  Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

  mcf-7 tumor lung oral sanger solexa gistic

• A sequence-based survey of the complex structural organization of tumor genomes.

  PMID 18364049 · PMC2397511 · Genome biology · 2008 · 8 claims · 6 setups

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  End sequencing profiling (ESP) can identify all classes of genome rearrangements in tumor genomes by paired-end sequencing of BAC clones

  tumors breast bac bt474 bac low-coverage fluorescence

• Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

  PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

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  Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

  erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex

• Detection of germline BRCA1 mutations by Multiple-Dye Cleavase Fragment Length Polymorphism (MD-CFLP) method.

  PMID 11556835 · PMC2375072 · British journal of cancer · 2001 · 6 claims · 4 setups

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  MD-CFLP can detect DNA sequence alterations (single-base substitutions, small insertions/deletions) in BRCA1 fragments longer than 1 kb

  brca1 direct pcr multiple-dye