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).

• New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

  PMID 16340004 · PMC1310899 · Nucleic acids research · 2005 · 7 claims · 8 setups

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  Long pure palindromes (>~200 bp) cannot be stably cloned in E.coli due to cruciform-driven instability, and no E.coli mutant fully overcomes this cloning block.

  individuals e.coli cerevisiae yeast pcr plasmid phi-29

• Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

  PMID 17264116 · PMC1851657 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cruciform extrusion propensity of PATRRs depends on both length and central symmetry of the repeat.

  plasmids same single-stranded patrr-containing cruciform endonuclease secondary

• Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways.

  PMID 16186129 · PMC1236719 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Targeted pso-TFO genomic crosslinks resolve via genetically separable pathways leading to either base substitutions or deletions.

  cho same uv41 6-tg small sequencing

• The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

  PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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  The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

  coli hep-2 pslm862 eaec colony hep-2 pcr

• Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

  PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

  coli plasmids plasmid white plasmid sequencing non-b

• Development of a Premature Stop Codon-detection method based on a bacterial two-hybrid system.

  PMID 16948859 · PMC1569827 · BMC biotechnology · 2006 · 7 claims · 7 setups

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  pREAL, fusing cya fragments T25 and T18 around a cloning site, produces catalytically active adenylate cyclase only when the inserted human DNA lacks a PSC

  coli brca1 colony bth102 bacterial mutagenic heterozygosity

• Protocol for assessing regulatory elements in murine heart using an AAV9-based massively parallel reporter assay.

  PMID 40252222 · PMC12033988 · STAR protocols · 2025 · 8 claims · 5 setups

  Has reproduction · 93

  An AAV9-based in vivo MPRA (AAV-MPRA) workflow, combined with a companion informatics platform, can dissect and quantify enhancer activity in mouse heart.

  agilent stbl3 hek293t wild-type self-annealing restriction plasmid

• Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

  PMID 12615897 · PMC2193825 · The Journal of experimental medicine · 2003 · 8 claims · 8 setups

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  Artemis-deficient ES cells are severely impaired in VDJ coding joining but retain relatively normal RS (signal) joining

  recombined southern rt-pcr colony

• Assisted large fragment insertion by Red/ET-recombination (ALFIRE)--an alternative and enhanced method for large fragment recombineering.

  PMID 17517785 · PMC1904275 · Nucleic acids research · 2007 · 6 claims · 7 setups

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  ALFIRE allows insertion of any fragment into small or large episomes without requiring an antibiotic selection gene in the final construct

  coli psc101badγβαa[hygro] psc101badγβαa-i-scei[amp] i-scei-cs-hmlhcgr-bac bacterial restriction pcr

• High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

  PMID 17702760 · PMC2018616 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  An integrated strategy combining en masse pentapeptide insertion mutagenesis, yeast two-hybrid screening, and parallel genetic footprinting can map protein-protein interfaces at amino acid precision and is generally applicable to any interacting protein pair.

  saccharomyces plasmid pooled individual yeast pcr-based restriction

• Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

  PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

  coli flp il10 flp-holliday recombination site-specific computational

• Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

  PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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  The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

  monocytogenes additional food j774 whole-genome comparative pcr