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).

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

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

  Full-text index only

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

  plasmids same single-stranded patrr-containing cruciform endonuclease secondary

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

  PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 8 setups

  Has reproduction · 86

  Of the four most frequent plasmid types, types II and III have more stable size, larger core genomes, and track the chromosomal phylogeny (more vertical transmission), while types I and IV (pSym) vary in size and gene content with phylogenies consistent with frequent horizontal transmission.

  clover-associated plasmids plasmidome replicons long-read k-mer genome

• LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

  PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups

  Has reproduction · 86

  LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.

  zymobiomics assembled assembler-generated novo reference-based contig

• Primase-based whole genome amplification.

  PMID 18559358 · PMC2490742 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  A primase-based Whole Genome Amplification (pWGA) method was developed using T7 gp4 primase to synthesize primers on-template, removing the requirement for synthetic primers

  genomic plasmids circular agarose picogreen dye-terminator

• The use of multiple displacement amplification to amplify complex DNA libraries.

  PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation

  hes3 hes3-derived coli plasmids isolation flcdna gis-pet

• Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

  PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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  E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

  e2348 hep-2 blast colony transformation

• Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.

  PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups

  Has reproduction · 68

  The complete genome of L. plantarum ZLP001 comprises a single 3,164,369 bp circular chromosome (GC 44.65%) plus seven plasmids (A–G), encoding 3,264 protein-coding sequences.

  lactobacillus plantarum whole-genome novo gene

• Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats.

  PMID 17142224 · PMC1669776 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Pure (GAA·TTC)44+ alleles at the FXN locus are unstable in human somatic cells in vivo, showing both expansions and contractions.

  blood v34a cos1 cv1 small genome-wide strip

• 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

• Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

  PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

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  Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

  minimally-passaged pylori coli arginase urease heterologous