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).

• Molecular characterization of retinitis pigmentosa in Saudi Arabia.

  PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups

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  The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.

  blood-derived families pcr-amplified ethnically genome-wide linkage bidirectional

• Association of polymorphisms in cyclooxygenase (COX)-2 with coronary and carotid calcium in the Diabetes Heart Study.

  PMID 18768181 · PMC2699582 · Atherosclerosis · 2009 · 8 claims · 6 setups

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  COX-2 promoter SNP rs689466 is associated with lower coronary calcified plaque (CorCP)

  whole-blood-derived subjects dhs unrelated snp coronary carotid

• Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species.

  PMID 34435438 · PMC9290141 · Molecular ecology resources · 2022 · 6 claims · 6 setups

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  Bisulphite conversion of unmethylated cytosines to thymines violates strand-complementarity assumptions of SNP callers and confounds true C->T SNPs with unmethylated cytosines, complicating SNP calling from bisulphite sequencing data.

  blood bismark-aligned bwa-mem-based gem3-based whole-genome snp

• VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic arthritis.

  PMID 17204151 · PMC1781940 · BMC musculoskeletal disorders · 2007 · 7 claims · 5 setups

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  The T allele of VEGF +936 (rs3025039) is significantly less frequent in PsA cases than in controls, suggesting a protective effect against PsA.

  blood same subject psa snp allele hardy-weinberg

• A common haplotype within the PON1 promoter region is associated with sporadic ALS.

  PMID 18618303 · PMC2739087 · Amyotrophic lateral sclerosis : official publication of the World Federation of Neurology Research Group on Motor Neuron Diseases · 2008 · 7 claims · 6 setups

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  Two SNPs (rs987539 in PON2 intron 6 and rs2074351 upstream of PON1 exon 2) within the paraoxonase gene cluster are significantly associated with susceptibility to sporadic ALS

  genomic case-control sporadic serum snp allelic sliding-window

• Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

  PMID 20021669 · PMC2803178 · BMC genetics · 2009 · 8 claims · 8 setups

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  WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays

  wga non-amplified archived serum-derived snp purification whole-genome

• Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

  PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

  tumor each rna-seq whole-genome targeted pcr-based

• Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

  PMID 19075497 · PMC4771609 · Journal of epidemiology · 2008 · 7 claims · 6 setups

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  Increasing the number of typed SNP loci does not necessarily improve prediction power, at least for the MTHFR gene

  healthy genomic genotype trial randomized snp haplotype

• Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

  PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

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  IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

  population blood genomic hapmap snp survival allele

• Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis.

  PMID 18635889 · PMC2556453 · American journal of respiratory and critical care medicine · 2008 · 7 claims · 5 setups

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  The TLR1 −7202A/G (rs5743551) G allele is associated with elevated TLR1-mediated cytokine production ex vivo

  blood expressing intensive patients tlr-agonist nf-κb surface

• Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome.

  PMID 34561431 · PMC8463674 · Nature communications · 2021 · 8 claims · 7 setups

  Has reproduction · 100

  revTWMR, a reverse transcriptome-wide Mendelian Randomization approach integrating GWAS and whole-blood trans-eQTL summary statistics, is proposed to estimate the causal effect of a phenotype on gene expression.

  blood ra-associated genome-wide revtwmr transcriptome-wide reverse functional

• Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.

  PMID 33461502 · PMC7812657 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 5 setups

  Has reproduction · 90

  Gene expression, exon expression, and intron excision ratio (splicing) molecular phenotypes are significantly heritable in sheep liver and muscle

  liver sheep sequencing snp heritability

• In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

  PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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  A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

  genomic genome pan blood snp sequence cross-species

• SNP-specific extraction of haplotype-resolved targeted genomic regions.

  PMID 18611953 · PMC2528194 · Nucleic acids research · 2008 · 6 claims · 4 setups

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  SNP-specific extraction isolates haploid genomic DNA flanking targeted SNPs by hybridizing an allele-specific oligo, enzymatically extending it with biotinylated nucleotides, and capturing the tagged allele with streptavidin-coated magnetic particles.

  genomic diploid quantitative sanger low

• Single-molecule sequencing of an individual human genome.

  PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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  Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

  genome staphylococcus single-molecule snp sanger

• Genetic variants of surfactant proteins A, B, C, and D in bronchopulmonary dysplasia.

  PMID 17264398 · PMC3850613 · Disease markers · 2006 · 7 claims · 4 setups

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  Significant associations (p ≤ 0.01) were found between BPD subgroups and alleles of SP-B and SP-B-linked microsatellite markers, and haplotypes of SP-A, SP-D, and SP-B

  greek genomic family-based pyrosequencing pcr

• Geographical genomics of human leukocyte gene expression variation in southern Morocco.

  PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

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  Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.

  peripheral blood genotype randomly genome-wide population admixture

• Familial pulmonary alveolar proteinosis caused by mutations in CSF2RA.

  PMID 18955570 · PMC2585845 · The Journal of experimental medicine · 2008 · 7 claims · 8 setups

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  Familial primary PAP is caused by compound heterozygous mutations in CSF2RA: a paternal G174R point mutation and a maternal 1.6-Mb deletion at Xp22.33 encompassing CSF2RA.

  peripheral pbmc blood lung flow western gm-csf