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).

• 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

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

  PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups

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  Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid

  bxpc-3 2-d maldi-tof-ms western

• Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

  PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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  Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

  genomic postmortem nimhgi esr1 targeted case-control family-based

• Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

  PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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  Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

  european african individuals nondiabetic snp variant direct

• Analysis of X chromosome inactivation in autism spectrum disorders.

  PMID 18361425 · PMC4867005 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 6 claims · 5 setups

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  No significant excess of skewed XCI was found in mothers of children with ASD or in affected girls compared to controls

  genomic multiplex mecp2 four chromosome non-parametric mutation

• Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

  PMID 18205922 · PMC2374452 · Arthritis research & therapy · 2008 · 7 claims · 4 setups

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  A standardized 3D in vitro alginate bead model of chondrocytes stimulated with synovial fibroblast supernatants can be used to profile RA-related cartilage destruction genes

  sv40 articular differentially antibody-based oligonucleotide real-time

• P19 H-ras induces G1/S phase delay maintaining cells in a reversible quiescence state.

  PMID 20046837 · PMC2798614 · PloS one · 2009 · 8 claims · 8 setups

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  p19 regulates telomerase activity through its interaction with p73α/β proteins

  yeast hela yeast facs pkc

• Mesotrypsin promotes malignant growth of breast cancer cells through shedding of CD109.

  PMID 20035377 · PMC2929293 · Breast cancer research and treatment · 2010 · 8 claims · 8 setups

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  Serine protease inhibitors (aprotinin, SBTI) cause morphological reversion of malignant T4-2 breast cancer cells in 3D culture, restoring acinar structure and basal polarity

  hmt-3522 organotypic quantitative lentiviral

• The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

  PMID 19956657 · PMC2777318 · PloS one · 2009 · 6 claims · 4 setups

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  The FOXL2 c.402C>G mutation is not commonly found in a wide variety of other cancers and is likely pathognomonic for A-GCTs and closely related tumors.

  tumor ovarian kgn high sanger taqman

• Interaction of vitamin D receptor with HLA DRB1 0301 in type 1 diabetes patients from North India.

  PMID 19956544 · PMC2780726 · PloS one · 2009 · 8 claims · 6 setups

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  Interaction between VDR and HLA alleles is mediated by a VDRE present in the promoter region of HLA-DRB1*0301, which may be detrimental in the absence of 1,25-(OH)2D3 in early childhood.

  blood genotype hla-drb1*0301 drb1*0301-carrying pcr-rflp pcr haplotype

• 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

  PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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  3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

  brain hbrr topo-cloned tag microarray quantitative

• Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers.

  PMID 19893615 · PMC2764086 · PloS one · 2009 · 8 claims · 8 setups

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  Simultaneous analysis of 347 thyroid samples across 12 histological classes from six datasets improves definition of diagnostic markers compared to prior binary-class studies

  thyroid microarray gene real-time

• Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.

  PMID 19889237 · PMC2783166 · BMC genomics · 2009 · 8 claims · 8 setups

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  scNT-MUC exhibit complete occlusive thrombi and absence of columnar epithelial layers not seen in control or scNT-N umbilical cords

  umbilical porcine puvec histology immunostaining real-time

• Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

  PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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  Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

  msi-h computational rb1cc1 normal pcr nonlinear real-time

• 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

• A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

  PMID 19864672 · PMC2793117 · The New England journal of medicine · 2009 · 7 claims · 7 setups

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  A homozygous CARD9 point mutation (Q295X, premature termination codon) is associated with autosomal recessive susceptibility to chronic mucocutaneous candidiasis.

  family patients peripheral-blood peripheral snp microsatellite sanger

• Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

  PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

  Has reproduction · 93

  24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

  jatropha geo bulk semi-quantitative quantitative

• Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

  PMID 19844207 · PMC2797562 · Molecular psychiatry · 2010 · 8 claims · 7 setups

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  rs1344706 in ZNF804A is associated with schizophrenia in the Irish ICCSS sample, replicating the original Cardiff finding

  irish iccss postmortem genomic snp haplotype logistic

• An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

  PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups

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  An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.

  lung hpl1d rrna external pcr rt-pcr quantitative