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).

• Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

  PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups

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  Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome

  squamous ophid degs oligonucleotide interaction connectivity

• Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

  PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

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  A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

  carcinoma derivative xenograft custom quantitative

• Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

  PMID 18182341 · PMC7129792 · Taiwanese journal of obstetrics & gynecology · 2007 · 6 claims · 5 setups

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  Oligonucleotide microarray and cDNA microarray are the two main microarray platforms used to study gene expression genome-wide.

  cervical cdna microarray combinatorial

• Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

  PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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  Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

  nb4 tf1 tracheobronchial moser affymetrix cdna microarray

• Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

  PMID 12962547 · PMC212256 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  RMA-generated gene expression values are markedly less variable and more reliable than MAS5.0- and MBEI-derived values

  postmortem oligonucleotide real-time quality

• Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.

  PMID 15099405 · PMC411067 · BMC bioinformatics · 2004 · 7 claims · 2 setups

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  Two-way ANOVA and Mack-Skillings tests on probe-level data with FDR control are substantially more powerful than t-test/Wilcoxon on probe-set level data for detecting differential expression

  fibroblast background high-density

• Toxicogenomics research consortium sails into uncharted waters.

  PMID 12460811 · PMC1241122 · Environmental health perspectives · 2002 · 8 claims · 8 setups

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  The NIEHS-funded $37 million Toxicogenomics Research Consortium (TRC) combines the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to define genetic variability, set gene expression standards, and study environmental stress responses.

  strains nervous mice liver microarray gene toxicogenomic

• Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

  PMID 16079153 · PMC4729368 · Development (Cambridge, England) · 2005 · 7 claims · 7 setups

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  Neocortical progenitor cells show rostrocaudal gradients of gene expression rather than discrete domains/compartments

  neocortex dorsal cortex embryo oligonucleotide microarray non-isotopic

• 'Genome design' model and multicellular complexity: golden middle.

  PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

  normal genes proteins encoded oligonucleotide gene functional

• Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

  PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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  Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

  liver genomic hcv-infected agilent two-color semi-quantitative real-time

• Functional genomics of early cortex patterning.

  PMID 16515721 · PMC1431711 · Genome biology · 2006 · 7 claims · 6 setups

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  The neocortical protomap is established as continuous rostro-caudal gradients of gene expression in progenitor cells, not discrete compartments

  neocortex embryonic fgfr1-mutant cortex oligonucleotide situ microarray

• Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

  PMID 20028558 · PMC2803201 · BMC genomics · 2009 · 8 claims · 7 setups

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  High expression of IL-8 and SLC1A3, identified via cross-species mining, is associated with poor outcome in an independent population of human osteosarcoma patients

  canine osteosarcoma independent third oligonucleotide cross-species quantitative

• Organismal complexity, cell differentiation and gene expression: human over mouse.

  PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

  human-mouse oligonucleotide exon comparative

• 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

• Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

  PMID 17888167 · PMC2082044 · BMC genomics · 2007 · 8 claims · 6 setups

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  A proposed coupled two-way clustering (CTWC/SPC) method combined with a GO-based functional concept consistency score can identify compact, robust gene subsets that define clinically meaningful DLBCL subtypes

  dlbcl identified microarray oligonucleotide coupled

• Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

  PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

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  Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

  pediatric same oligonucleotide quantitative

• New center a stroke of gene-ius.

  PMID 11171539 · PMC1242068 · Environmental health perspectives · 2001 · 8 claims · 4 setups

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  Exposure to alkylating agents evokes at least three-fold expression changes in about one-third of the yeast genome (~2,000 genes), far beyond DNA repair genes alone

  yeast genomic microarray northern custom

• Asthma investigators begin to reap the fruits of genomics.

  PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

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  Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

  monkey models lung inbred cdna oligonucleotide northern

• Sox8 remodels the cranial ectoderm to generate the ear.

  PMID 35867760 · PMC9282420 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Sox8 sits at the top of a core transcriptional circuit (Sox8, Pax2, Lmx1a, Zbtb16) that determines otic identity

  chick bulk single-cell chipseq

• Using DNA microarrays to study host-microbe interactions.

  PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

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  DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

  streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene