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).

• Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

  PMID 18281252 · PMC2443276 · Carcinogenesis · 2008 · 7 claims · 4 setups

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  Cigarette smoking is associated with a higher frequency of somatic mtDNA mutations in buccal cells

  buccal subject ttge real-time pcr-based

• Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

  PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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  A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

  bovine pcr-based comparative rt-pcr

• Genetic variation in PARL influences mitochondrial content.

  PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

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  PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

  genomic nuclear parl pcr snp real-time

• Alteration of the copy number and deletion of mitochondrial DNA in human hepatocellular carcinoma.

  PMID 15150555 · PMC2409531 · British journal of cancer · 2004 · 8 claims · 5 setups

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  mtDNA copy number and the content of mitochondrial respiratory proteins are reduced in HCC tumor tissue compared with corresponding non-tumorous liver.

  hcc competitive quantitative immunoblot

• Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

  PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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  The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

  dog hamster pcr primer pcr blast sequence

• Frequency and spectrum of c-Ki-ras mutations in human sporadic colon carcinoma, carcinomas arising in ulcerative colitis, and pancreatic adenocarcinoma.

  PMID 1773797 · PMC1568060 · Environmental health perspectives · 1991 · 8 claims · 7 setups

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  60% (37/61) of sporadic colon carcinomas contain c-Ki-ras codon 12 mutations

  sporadic carcinoma pancreatic tumor pcr flow mixing

• RPS4Y gene family evolution in primates.

  PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

  primate chromosomes rps4x concatenated pcr fluorescence repeat

• Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress.

  PMID 36618608 · PMC9815118 · Frontiers in plant science · 2022 · 8 claims · 8 setups

  Has reproduction · 75

  Chilling stress significantly alters the ratio of anthocyanins, chlorophylls, and carotenoids, causing leaf color to change from green to purple

  japonica arabidopsis pigment bulk functional

• TP53 mutation analyses on breast carcinomas: a study of paraffin-embedded archival material.

  PMID 8761369 · PMC2074687 · British journal of cancer · 1996 · 8 claims · 8 setups

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  CDGE can be used to successfully detect TP53 mutations (exons 5-8) in DNA extracted from archival paraffin-embedded breast carcinoma tissue

  archival pcr breast tumour pcr-cdge direct restriction

• Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

  PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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  Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

  parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr

• Sequence determinants of human microsatellite variability.

  PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups

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  Mean and maximum number of repeats across individuals are positively correlated with heterozygosity

  hgdp-ceph genome calibrated microsatellite blastn sequence

• The D2 dopamine receptor gene and nicotine dependence among bladder cancer patients and controls.

  PMID 19842028 · PMC3719969 · Behavior genetics · 2010 · 8 claims · 5 setups

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  Among ever-smoking controls, A1 and B1 genotypes were associated with greater smoking intensity and younger age at smoking initiation than A2A2/B2B2

  peripheral bladder current genotype pcr-rflp structured fagerström

• Helicobacter Pylori's plasticity zones are novel transposable elements.

  PMID 19727398 · PMC2731543 · PloS one · 2009 · 8 claims · 8 setups

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  Plasticity zones are a novel class of transposable elements (named TnPZs), flanked by direct repeats of 5'AAGAATG and inserted at multiple discrete chromosomal sites

  pylori shimaa model mammalian pcr-based genome pcr

• Mutation analysis of congenital cataract in a Basotho family identified a new missense allele in CRYBB2.

  PMID 19649175 · PMC2718852 · Molecular vision · 2009 · 8 claims · 6 setups

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  A heterozygous missense mutation c.607G>A in exon 6 of CRYBB2, causing p.Val187Met, is the probable causative mutation for congenital nuclear cataract in this family

  genomic basotho pcr restriction secondary

• Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

  PMID 33967968 · PMC8100199 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

  Has reproduction · 73

  An undergraduate CURE combining field sampling, wet-lab microbiology, and genomic bioinformatics can be used to isolate and characterize environmental S. enterica strains.

  putative enterica selected assembled endpoint genome long-read

• Molecular genetic evidence for unifocal origin of advanced epithelial ovarian cancer and for minor clonal divergence.

  PMID 7577492 · PMC2033953 · British journal of cancer · 1995 · 7 claims · 4 setups

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  LOH analysis has higher sensitivity than DNA flow cytometry for detecting unifocal origin of bilateral ovarian tumors

  bilateral paraffin-embedded ovarian peripheral loh flow isolation

• Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

  PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

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  Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold

  simulated real chromosome randomly simulation multiplex coverage-vs-n

• A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

  PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

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  HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

  giardia serial northern western

• Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

  PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups

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  MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution

  mip diagnostic is900-specific pgg

• In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

  PMID 17726045 · PMC2094079 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Two exonic mutations, PINK1 E417G and PARK7 E64D, disrupt binding to U1 snRNA and cause skipping of the mutation-harboring exon

  hek293 genome lymphocytes minigene artificial genome-wide