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).

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.

  PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids

  coli st58 novo draft whole-genome pan-genome-wide plasmid

• Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

  PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups

  Has reproduction · 79

  196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions

  rhizobium strains genotype genome whole-genome orthologous snp

• Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

  PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups

  Has reproduction · 44

  Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.

  plasmid coli wild-type artificial smrt read-mixing distributional

• Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

  PMID 17284462 · PMC1865043 · Nucleic acids research · 2007 · 6 claims · 6 setups

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  Cryptic lox P sites occur frequently and are homogeneously distributed across the mouse genome (1.2 primary sites per megabase).

  genome bac coli el350 genome-wide sequence bacterial

• Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.

  PMID 36752777 · PMC9997745 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 89

  Dogs are the dominant host of E. coli ST372, and clusters within the ST372 population structure exhibit distinctive O:H types.

  coli st372 core draft whole-genome core population

• Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

  PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

  hela hs578t nih3t3 genomic chap-chip conventional scanning

• 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

• The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

  PMID 30899024 · PMC6428865 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 85

  Xrn1 promotes translation of a specific group of transcripts encoding membrane proteins

  cerevisiae western renilla polysome

• Viral and host determinants of RNA virus vector replication and expression.

  PMID 15734041 · PMC7115378 · Vaccine · 2005 · 7 claims · 4 setups

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  BMV RNA replication occurs in a virus-induced, membrane-bounded compartment rather than in the open cytoplasm.

  bmv saccharomyces wild-type immunogold genome-wide northern

• Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

  PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

  Has reproduction · 67

  Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

  vibrio coli anguillarum transposon-insertion conjugative functional

• The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.

  PMID 35371105 · PMC8964954 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  HCV E1E2 glycoproteins, and more so E2, down-modulate HIV-1 LTR activation in 293T, TZM-bl and Huh7 cells

  293t tzm-bl tzm-bl-e1e2 hiv-1 pseudo-typed transcriptomic