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).

• TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

  PMID 16229746 · PMC1276789 · BMC cancer · 2005 · 8 claims · 4 setups

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  Survival for BRCA1-familial ovarian cancer cases with TP53 mutations was not significantly different from familial cases without TP53 mutations (p=0.25, RR=1.64)

  ovarian sporadic paraffin-embedded mutation survival extraction

• Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

  PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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  Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

  lung wild-type matched paired two-round real-time airs-rflp

• TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

  PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 69

  TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.

  ppm1d-transgenic genome genome read touchdown-pcr

• LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

  PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

  schizosaccharomyces pombe rna-seq lasso lariat-specific

• 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

• Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

  PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

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  Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

  peripheral mhc2ta pcr sanger bisulfite cpg

• Comprehensive molecular etiology analysis of nonsyndromic hearing impairment from typical areas in China.

  PMID 19744334 · PMC2754984 · Journal of translational medicine · 2009 · 8 claims · 8 setups

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  GJB2 mutations account for 18.31% (52/284) of patients with nonsyndromic hearing loss

  peripheral patients mtdna slc26a4 pcr pcr-based sanger

• A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction.

  PMID 19956411 · PMC2786888 · Molecular vision · 2009 · 6 claims · 7 setups

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  A novel de novo heterozygous nonsense mutation (c.413C>G, p.S138X) in OTX2 causes an early onset retinal dystrophy accompanied by pituitary dysfunction (growth hormone deficiency)

  genomic anonymous single direct lca mismatch

• Coxiella burnetii genotyping.

  PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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  Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

  coxiella burnetii matrix sequence pcr molecular pcr-based

• Genotypic analysis of two hypervariable human cytomegalovirus genes.

  PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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  UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

  hcmv clinical pcr ul146 pcr nested molecular

• Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

  PMID 19835606 · PMC2784330 · Genome biology · 2009 · 7 claims · 2 setups

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  Hybrid selection of cDNA dramatically increases the specificity of sequencing reads mapping to targeted cancer-related transcripts.

  k-562 targeted sanger

• A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

  PMID 15238985 · PMC2364794 · British journal of cancer · 2004 · 7 claims · 6 setups

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  A novel A-1012G (adenine-guanine) polymorphism exists in the VDR exon 1a promoter region, identified by SSCP screening and sequencing

  blood variant patients same sscp sanger pcr-rflp

• MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

  PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

  pooled genomic aneuploid dog mlga

• Geographic distribution and genetic diversity of the Ehrlichia sp. from Panola Mountain in Amblyomma americanum.

  PMID 18433500 · PMC2394526 · BMC infectious diseases · 2008 · 8 claims · 6 setups

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  PME was not recently introduced to the United States, given its extensive geographic distribution, multi-year persistence at sites, and genetic variability

  amblyomma pme-positive map1 nested pcr sanger

• Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa.

  PMID 19656662 · PMC2744841 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

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  Pyrosequencing™ can substitute for traditional sequencing methods, providing rapid (<1 h) and reliable detection of antibiotic resistance mutations in P. aeruginosa

  clinical extracted pcr fluoroquinolone-resistant kirby–bauer multiplex sanger

• Genome amplification of single sperm using multiple displacement amplification.

  PMID 15942023 · PMC1143700 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  MDA was applied for the first time to whole-genome amplification of single sperm cell DNA

  single sperm pcr sanger real-time

• Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.

  PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups

  Has reproduction · 63

  The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.

  balb cl-sl donovani experimental transgenic genome

• CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

  PMID 31365872 · PMC6684324 · Cell reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Genome-wide CRISPR/Cas9 screening in Daudi B cells using CD40L-induced Fas upregulation as a readout identifies both positive and negative regulators of CD40

  daudi splenic genome-wide immunoblot qpcr

• A novel mutation in GRK1 causes Oguchi disease in a consanguineous Pakistani family.

  PMID 19753316 · PMC2742643 · Molecular vision · 2009 · 8 claims · 6 setups

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  A novel nonsense mutation (c.614C>A; p.S205X) in exon 1 of GRK1 causes disease in family RP19

  affected family rp19 selected genome-wide microsatellite direct