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).

• 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

• Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR.

  PMID 17439964 · PMC1888819 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Bisulfite treatment causes DNA strand breakage (via abasic site formation and beta-elimination) in addition to cytosine deamination.

  genomic synthetic bisulfite-treated cloned methylation-sensitive quantitative gel

• Clinical practice and genetic counseling for cystic fibrosis and CFTR-related disorders.

  PMID 19092437 · PMC2810953 · Genetics in medicine : official journal of the American College of Medical Genetics · 2008 · 8 claims · 5 setups

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  CFTR-related disorders form a disease spectrum ranging from isolated congenital absence of the vas deferens (CAVD) to multiorgan classic cystic fibrosis (CF).

  patients newborns sweat transepithelial cftr

• An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

  PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

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  A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

  lung known leukemia tumor paired-end computational snp

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

  PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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  Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

  archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr

• Re-evaluating early breast neoplasia.

  PMID 18279539 · PMC2374963 · Breast cancer research : BCR · 2008 · 8 claims · 7 setups

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  The classic single linear model of breast cancer progression requires revision based on high-throughput molecular genetic and gene expression data.

  dcis breast patient-matched premalignant comparative combined cdna

• Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

  PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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  Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

  homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular

• A new era for proteomics research?

  PMID 19014405 · PMC2614486 · Genome biology · 2008 · 8 claims · 8 setups

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  Refined mass spectrometry instrumentation and software now make whole-proteome coverage of model organisms in a single experiment conceivable

  proteins lines kinases breast mass silac kinase-specific

• Structural modeling and functional characterization of a novel gain-of-function TLR8 variant causing severe inflammatory syndrome.

  PMID 41729082 · PMC12956005 · JCI insight · 2026 · 8 claims · 8 setups

  Has reproduction · 89

  TLR8 A518T is a gain-of-function variant that enhances NF-κB activation and increases secretion of proinflammatory cytokines upon stimulation compared with WT TLR8

  plasma pbmcs expressing tlr8 targeted plasma quantitative

• Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

  PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 44

  The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI

  spinal brown sci microarray functional protein-protein

• Proteomic characterization of plasma-derived clotting factor VIII-von Willebrand factor concentrates.

  PMID 19768705 · PMC3030255 · Electrophoresis · 2009 · 8 claims · 8 setups

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  Commercial plasma-derived FVIII/VWF concentrates contain significant amounts of non-FVIII/VWF plasma proteins as impurities

  plasma-derived octanate sec fviii sds-page size-exclusion lc-esi-ms

• Metabolic syndrome: from epidemiology to systems biology.

  PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

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  MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

  populations rats adipose four genome-wide linkage gene

• Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

  PMID 18654835 · PMC4973579 · Biogerontology · 2009 · 8 claims · 7 setups

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  Treatment of HCA3 human diploid fibroblasts with a mild dose of H2O2 (600 μM) induces premature senescence without killing the cells.

  hca3 differentially mudpit cdna semi-quantitative

• Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

  PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

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  The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

  cerevisiae mitocarta mitochondrial tissues comparative subcellular gene

• Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

  PMID 19880432 · PMC2780955 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 8 claims · 5 setups

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  Identified 23,241 human genes transcribed into protein-coding mRNAs using full-length cDNA and 5'-EST sequence data

  tissues genome full-length genes full-length genome orf

• Use of proteomics for validation of the isolation process of clotting factor IX from human plasma.

  PMID 19819359 · PMC2818390 · Journal of proteomics · 2010 · 8 claims · 8 setups

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  Proteomic techniques (LC-MS/MS, iTRAQ, immunochemical/biochemical methods) can monitor and validate each production step of pd F IX isolation

  plasma in-process chromatographic one-stage competitive elisa

• Malaria genomics meets drug-resistance phenotyping in the field.

  PMID 19664295 · PMC2745762 · Genome biology · 2009 · 8 claims · 8 setups

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  Significantly longer parasite clearance times in Pailin (western Cambodia) versus Wang Pha (Thailand-Myanmar border) establish the presence of artemisinin resistance in western Cambodia.

  falciparum plasmodium drug clinical high-throughput

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage