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

• The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

  PMID 20368178 · PMC2894525 · Science translational medicine · 2009 · 7 claims · 6 setups

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  Germ-free C57BL/6J mice can be stably and heritably colonized with a human fecal microbiota, reproducing much of the donor's bacterial diversity.

  fecal postnatal luminal pooled 16s shotgun body

• Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

  PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

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  BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

  serum-derived tumour serum ht29 arms sanger topo

• Genetic differences between avian and human isolates of Candida dubliniensis.

  PMID 19788816 · PMC2819872 · Emerging infectious diseases · 2009 · 7 claims · 6 setups

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  13 of 14 avian-associated C. dubliniensis isolates form a genetically distinct subgroup within MLST clade C1, separate from human isolates

  candida fecal avian-associated multilocus pcr multiplex

• The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.

  PMID 38537644 · PMC11063626 · Cell reports · 2024 · 8 claims · 8 setups

  Has reproduction · 62

  The natural (non-sterilized) Clue Field soil microbiome reduces Striga attachment to sorghum roots compared to gamma-sterilized soil

  clue sorghum striga 16s striga germination

• Mutational spectrum of p53 gene in arsenic-related skin cancers from the blackfoot disease endemic area of Taiwan.

  PMID 10362120 · PMC2363055 · British journal of cancer · 1999 · 7 claims · 4 setups

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  p53 gene mutation rate is high in arsenic-related skin cancers (39% Bowen's disease, 28.6% BCC, 55.6% SCC)

  skin fresh-frozen pcr-sscp direct immunohistochemistry

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• Characterisation of p53 status at the gene, chromosomal and protein levels in oesophageal adenocarcinoma.

  PMID 14583777 · PMC2394414 · British journal of cancer · 2003 · 8 claims · 4 setups

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  p53 gene mutations are infrequent in oesophageal adenocarcinoma (9.6%)

  formalin-fixed oesophageal evaluable pooled rflp fluorescence immunohistochemistry

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic

• The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression.

  PMID 16573809 · PMC1450280 · BMC genomics · 2006 · 7 claims · 8 setups

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  MDA-amplified DNA does not introduce major distortion of copy number imbalance assignments compared to unamplified DNA in control CGH experiments.

  laser-capture-microdissected normal cancer fresh-frozen array gacgh laser

• BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).

  PMID 16439806 · PMC1356528 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  oaCGH, not BAC CGH arrays, is the platform that will prevail in the future

  genomic lung genetics bt474 array exon

• Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

  PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

  inhbb cloned same fresh-frozen rnase masscleave clonal

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• Mutational analysis of oncogenic AKT E17K mutation in common solid cancers and acute leukaemias.

  PMID 18392055 · PMC2391109 · British journal of cancer · 2008 · 7 claims · 8 setups

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  AKT1 E17K mutation occurs in breast cancers at a low frequency (4/93, 4.3%)

  breast colorectal gastric hepatocellular pcr-sscp capillary

• Novel syntaxin 11 gene (STX11) mutation in three Argentinean patients with hemophagocytic lymphohistiocytosis.

  PMID 19967551 · PMC7370861 · Journal of clinical immunology · 2010 · 8 claims · 8 setups

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  Three unrelated Argentinean HLH patients carry an identical novel homozygous 4-bp deletion (c.581_584delTGCC; p.Leu194ProfsX2) in STX11

  genomic peripheral blood fresh direct snp rt-pcr

• Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies.

  PMID 41503158 · PMC12770963 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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  A comprehensive comparison of seven 3'/whole-transcriptome single-cell platforms and two 5' whole-transcriptome + TCR platforms was performed using PBMCs from multiple donors.

  pbmcs sorted scrna-seq evercode

• Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

  PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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  Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

  apc-deficient heart ileum fresh-frozen spatial high-resolution bulk

• Single-cell lineage tracing identifies hemogenic endothelial cells in the adult mouse bone marrow.

  PMID 42043300 · PMC13120821 · eLife · 2026 · 8 claims · 8 setups

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  Adult bone marrow-resident Cdh5/VE-Cadherin+ endothelial cells produce hematopoietic cell progeny both in vitro and in vivo.

  bone lin sorted lethally flow confocal sorted-cell