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).

Publications 1.3k Datasets 392.5k Experiments 762

System / cell line: relative ✕ Clear

DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia.

PMID 19102774 · PMC2630979 · BMC medical genetics · 2008 · 8 claims · 6 setups

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Variation in SYN III distal CpG island methylation is not related to schizophrenia in the population sample or in a monozygotic twin pair discordant for schizophrenia

brain blood non-human semi-quantitative sodium bisulfite
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

PMID 18980691 · PMC2612029 · BMC genomics · 2008 · 8 claims · 8 setups

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mtDNA depletion confers specific, shared gene expression profiles in A549 cells grown in culture and as xenografts

a549 growth oxygen mtdna
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

PMID 18974882 · PMC2570797 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Midgut (oocyst-derived) and salivary gland sporozoite proteomes are markedly different despite near-identical morphology, consistent with their differing hepatocyte infectivity

falciparum berghei nano-lc-ms targeted gene
Apolipoprotein A-IV, a putative satiety/antiatherogenic factor, rises after gastric bypass.

PMID 18948973 · PMC2627784 · Obesity (Silver Spring, Md.) · 2009 · 6 claims · 7 setups

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Apolipoprotein A-IV (apo A-IV) is significantly increased in fasting plasma after RYGBP compared to pre-operative levels

fasting plasma itraq-labeled subjects itraq immunoblot sds-page
Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

PMID 18948297 · PMC2602764 · Nucleic acids research · 2008 · 6 claims · 8 setups

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Incorporating a biotin tag into the HTA probe enables purification of labeled heteroduplexes and direct sequencing of the separated query strand, allowing recovery of minor variant sequences

hiv-1 biotin-hta-purified original recovered heteroduplex rt-pcr sanger
Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements.

PMID 18942891 · PMC2570425 · PLoS biology · 2008 · 8 claims · 5 setups

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An unbiased SILAC-based proteomic screen identified a relatively small cohort of γ-secretase substrates among thousands of proteins in HeLa cells, all of which are type I transmembrane proteins.

hela presenilin-1 hek silac western
Adaptive history of single copy genes highly expressed in the term human placenta.

PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

term single same lists microarray comparative site
Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.

PMID 18839982 · PMC3204659 · Journal of proteome research · 2008 · 7 claims · 4 setups

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Golgi membrane protein 1 (GOLM1/GP73), Annexin IV, and Eps8 are validated candidate biomarkers for cholangiocarcinoma

membrane bile 18o-labeling sds-page western
Prevalence of variations in melanoma susceptibility genes among Slovenian melanoma families.

PMID 18803811 · PMC2556318 · BMC medical genetics · 2008 · 8 claims · 7 setups

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CDKN2A germline mutations were found in 7 of 25 (28.0%) Slovenian melanoma families

genomic relative p16ink4a pcr pearson student's
Short tandem repeats in human exons: a target for disease mutations.

PMID 18789129 · PMC2543027 · BMC genomics · 2008 · 8 claims · 6 setups

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STRs are present in exons of 92% of known human genes, unlike longer tandem repeats which are rare in exons

reference genome genes genome-wide indel disease
The impact of microRNAs on protein output.

PMID 18668037 · PMC2745094 · Nature · 2008 · 8 claims · 8 setups

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MicroRNA targeting for protein repression occurs primarily through seed-matched sites (6mer, 7mer-A1, 7mer-m8, 8mer) located in favourable predicted contexts within 3′ UTRs

hela neutrophils bone mir-223 quantitative blot microarray
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

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Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

salmonella sequenced typhi whole-genome snp-based selection
Strict sun protection results in minimal skin changes in a patient with xeroderma pigmentosum and a novel c.2009delG mutation in XPD (ERCC2).

PMID 18637129 · PMC2605190 · Experimental dermatology · 2009 · 8 claims · 5 setups

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Strict, rigorous sun protection starting at age 2 resulted in minimal skin disease (only mild lip freckling, no skin cancer) in XP2GO despite an XP diagnosis

fibroblasts xp2go post-uv host real-time
Bayesian survival analysis in genetic association studies.

PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

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A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

simulated same sanad bayesian univariate partial
Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.

PMID 18612418 · PMC2440534 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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Developed a firefly luciferase (fLUC) reporter gene assay to test for the presence of a viable RNAi pathway in helminth parasites

fasciola schistosoma electroporation-mediated rnai whole-mount
Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

PMID 18588689 · PMC2474586 · BMC medical genetics · 2008 · 8 claims · 6 setups

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A region spanning the gene RAI and the 5' portion of XPD is associated with postmenopausal breast cancer

peripheral genomic genotype independent linkage targeted genotyping
Genetic and biochemical studies in Argentinean patients with variegate porphyria.

PMID 18570668 · PMC2467414 · BMC medical genetics · 2008 · 8 claims · 6 setups

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All 18 studied VP patients harbored PPOX gene mutations in heterozygous state

peripheral blood relative urine pcr rt-pcr enzyme
Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories?

PMID 18557994 · PMC2481495 · Breast cancer research : BCR · 2008 · 8 claims · 8 setups

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Mutation frequencies in ATM, BRIP1, PALB2 and CHEK2 are many times higher in women with strong breast cancer family history (familial cases) than in population controls.

women familial finnish unselected germline international statistical
Upregulation of Copine1 in trabecular meshwork cells of POAG patients: a membrane proteomics approach.

PMID 18523666 · PMC2408776 · Molecular vision · 2008 · 7 claims · 5 setups

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Copine1 mRNA and protein expression are upregulated in glaucomatous TM (GTM) cells compared to normal TM (NTM) cells

trabecular ntm 2-d immunocytochemistry quantitative
Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

PMID 18477650 · PMC2443277 · Carcinogenesis · 2008 · 8 claims · 7 setups

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HBx C-terminal deletion mutants (HBx3'-30 and HBx3'-40) produce differentially expressed gene and protein profiles in transfected Huh7 HCC cells, mostly involving transcriptional regulation, oncogenes/tumor suppressors, cell junctions, signal transduction, metabolism and immune response

huh7 frozen hcc genomic cdna two-dimensional western

Experiments

DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia.

mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

Apolipoprotein A-IV, a putative satiety/antiatherogenic factor, rises after gastric bypass.

Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements.

Adaptive history of single copy genes highly expressed in the term human placenta.

Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.

Prevalence of variations in melanoma susceptibility genes among Slovenian melanoma families.

Short tandem repeats in human exons: a target for disease mutations.

The impact of microRNAs on protein output.

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Strict sun protection results in minimal skin changes in a patient with xeroderma pigmentosum and a novel c.2009delG mutation in XPD (ERCC2).

Bayesian survival analysis in genetic association studies.

Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.

Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

Genetic and biochemical studies in Argentinean patients with variegate porphyria.

Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories?

Upregulation of Copine1 in trabecular meshwork cells of POAG patients: a membrane proteomics approach.

Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.