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).

• Genetic variation of SARS coronavirus in Beijing Hospital.

  PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups

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  113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain

  clinical extracted rna-derived cloned nested screening direct

• Identification of recombinant human papillomavirus type 16 variants.

  PMID 19758676 · PMC2769496 · Virology · 2009 · 8 claims · 5 setups

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  Concurrent infection with 8 HPV16 variants (1 prototype/European, 6 recombinant clones, plus later African-2) was detected in a single woman via PCR-based cloning and sequencing

  cervical pcr-based recombinant-specific direct

• B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

  PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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  EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

  ebv-transformed cloned rt-pcr southern sequence

• Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

  PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

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  O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

  serum hbv full-length o-hbv nested phylogenetic quasispecies

• Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

  PMID 15867095 · PMC2213188 · The Journal of experimental medicine · 2005 · 7 claims · 6 setups

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  IgVH genes have evolved precise placement of coding-strand Cs so that AID-induced C-to-T mutations are predominantly silent, especially in the CDRs.

  igvh germline non-igv immunogenetics flow cdna bioinformatic

• Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

  PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

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  The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

  cloned clinical hominis pcr culture sanger

• The Neandertal genome and ancient DNA authenticity.

  PMID 19661919 · PMC2725275 · The EMBO journal · 2009 · 8 claims · 6 setups

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  Only direct assays of DNA sequence positions where Neandertals differ from all contemporary humans can reliably estimate human contamination.

  neandertal pcr high-throughput genome

• Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13).

  PMID 15234325 · PMC7129141 · International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2004 · 7 claims · 3 setups

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  Human aminopeptidase N (APN/CD13/ANPEP) is the receptor for human coronavirus 229E (HCoV-229E)

  genomic cloned consensus pcr molecular sequence

• Shotgun haplotyping: a novel method for surveying allelic sequence variation.

  PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

  genomic long pcr ampicillin-resistant long cloning short

• Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.

  PMID 17900363 · PMC2098775 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  M. ulcerans has evolved into five InDel haplotypes that separate into two distinct phylogenetic lineages: a 'classical' lineage (Africa, Australia, South East Asia) and an 'ancestral' lineage (Asia, South America, Mexico)

  ulcerans marinum plasmid-based pcr genome

• Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

  PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

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  HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

  plasma proviral cloned pbmc hiv-1 nested clonal

• The promise and reality of personal genomics.

  PMID 19723346 · PMC2768970 · Genome biology · 2009 · 7 claims · 6 setups

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  Despite being the most complete and accurate individually sequenced human genome to date, AK1 sequencing still misses a substantial fraction of variants, showing sequencing technology remains far from complete/reliable.

  ak1 six whole-genome copy-number genotyping-based

• A biomedically enriched collection of 7000 human ORF clones.

  PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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  Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

  genes mgc plasmid literature pcr sequence

• Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.

  PMID 32111840 · PMC7048732 · Nature communications · 2020 · 6 claims · 8 setups

  Has reproduction · 95

  SuSr-D1 encodes Med15b.D, a subunit of the conserved Mediator complex that regulates transcription of protein-coding genes.

  wheat cth chromosome ns1 stem adult-plant flow-sorted

• The role of p53 inactivation in human cervical cell carcinoma development.

  PMID 7841033 · PMC2033612 · British journal of cancer · 1995 · 8 claims · 7 setups

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  HPV DNA sequences were detected in 43 of 47 (91.5%) primary uterine cervical cancers

  formalin-fixed cervical p53 recurrent pcr southern pcr-single-strand

• Molecular analysis of Plasmodium ovale variants.

  PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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  P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

  ovale plasmodium pcr first comparative

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

  PMID 15673711 · PMC548376 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  A new technique combining whole-genome selective PCR amplification and subtractive hybridization can experimentally identify polymorphic retroelement insertions without prior knowledge of RE evolutionary history or sequence

  genomic driver coli individual whole-genome subtractive cloning

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

  PMID 18974839 · PMC2572839 · PloS one · 2008 · 7 claims · 6 setups

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  Pseudomonas 16S rDNA is significantly more prevalent in ileal biopsies of CD patients than non-IBD patients

  ileal p16s otu pseudomonas nested cloning