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).

• Functional genomics of the pregnant uterus: from expectations to reality, a compilation of studies in the myometrium.

  PMID 17570164 · PMC1892061 · BMC pregnancy and childbirth · 2007 · 8 claims · 6 setups

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  Differential expression of 118 genes across compiled myometrium studies could be distributed into 14 main KEGG pathways most representative of changes between NP, PTNIL, TNIL and TIL states

  myometrium compiled cdna oligonucleotide kegg

• Expression profiling of drug response--from genes to pathways.

  PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups

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  Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.

  blastocyst skin specified cortex pathway two-color microarray

• Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

  PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

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  Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

  blood pooled gene chip-chip conventional quantitative

• 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

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• The molecular characterization and clinical management of multiple myeloma in the post-genome era.

  PMID 19657360 · PMC3686133 · Leukemia · 2009 · 8 claims · 8 setups

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  GEP identifies distinct molecular subgroups of MM associated with differing clinical features and survival outcomes

  myeloma cd138-immunomagnetically plasma bone-marrow filter-based gene-expression targeted

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• Cancer-cell-secreted miR-204-5p induces leptin signalling pathway in white adipose tissue to promote cancer-associated cachexia.

  PMID 37620316 · PMC10449837 · Nature communications · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  Breast cancer cell-secreted exosomal miR-204-5p induces HIF1A in white adipose tissue by targeting the VHL gene.

  balb nsg ewat iwat orthotopic indirect sev

• Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

  PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)

  vero calu-3 genes direct pcr poly

• Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

  PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

  Has reproduction · 27

  A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

  radish assembled rna-seq novo functional

• Translating genome sequences into biological understanding.

  PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups

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  Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.

  embryonic transfectable drosophila computational gene-trap pooled cross-species

• The genome of Brugia malayi - all worms are not created equal.

  PMID 18952001 · PMC2668601 · Parasitology international · 2009 · 8 claims · 8 setups

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  Comparative genome analysis shows conserved long-range synteny but divergent local gene order between B. malayi and C. elegans, reflecting distinct evolutionary trajectories of parasitic and free-living lineages.

  malayi elegans wbm-infected filarial whole-genome genome-wide comparative

• Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

  PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

  Has reproduction · 70

  AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

  head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr

• Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

  PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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  Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

  saliva amplified extracted differentially genome quality extraction

• RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

  PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 41

  Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

  pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative

• 25th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, 10-14 December 2002 Update on preclinical and translational research.

  PMID 12631391 · PMC154153 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

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  Growth factor signalling (EGF/HER-2/MAPK, AKT) phosphorylates the oestrogen receptor and drives development of endocrine-resistant breast cancer

  xenograft serum frozen tumour xenograft mass cdna

• A European focus on proteomics.

  PMID 15128441 · PMC416463 · Genome biology · 2004 · 8 claims · 8 setups

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  MALDI-MS and ESI-MS are complementary techniques that identify overlapping but distinct subsets of proteins

  ribosomal breast ovarian prostate maldi-ms laser-capture fticr-ms

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Current and future directions in genomics of amyotrophic lateral sclerosis.

  PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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  Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

  american sals dutch irish genome laser expression

• Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

  PMID 18397877 · PMC2427143 · Human molecular genetics · 2008 · 8 claims · 8 setups

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  All six somatic TSC1 missense mutations found in bladder tumours cause loss of TSC1 function, but via distinct molecular mechanisms.

  hcv29 lines tsc1 bladder immunoblotting real-time co-immunoprecipitation