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).

• Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

  PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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  89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

  normalized rainbow salmonids microsatellite sanger pcr

• Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

  PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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  A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

  hamster testis predicted cdna northern comparative

• Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

  PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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  A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

  cdna image hbs1l ahi1 rt-pcr est northern

• 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

• Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.

  PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups

  Has reproduction · 63

  The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.

  balb cl-sl donovani experimental transgenic genome

• Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

  PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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  Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

  liver genomic tissues embryos rt-pcr genomic secondary

• Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

  PMID 9989976 · PMC2192941 · The Journal of experimental medicine · 1999 · 8 claims · 8 setups

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  The Lps locus was fine-mapped to a 0.9-cM interval spanning a 1.7-Mb genomic contig on mouse chromosome 4.

  c3h genomic bac multiple-tissue genetic yac direct

• Sources of variability and effect of experimental approach on expression profiling data interpretation.

  PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups

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  Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling

  skeletal muscle spleen myogenic affymetrix duplicate unsupervised

• Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

  PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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  A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

  bovine pcr-based comparative rt-pcr

• Targeted disruption of the S1P2 sphingosine 1-phosphate receptor gene leads to diffuse large B-cell lymphoma formation.

  PMID 19903857 · PMC2973841 · Cancer research · 2009 · 8 claims · 8 setups

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  S1P2−/− mice develop clonal B-cell lymphomas with age, with ~half affected by 1.5-2 years

  s1p2− lymphoma bone genomic necropsy histology flow

• The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

  PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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  The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

  genomic predicted cdna tissues genomic sequence pcr

• GENCODE: producing a reference annotation for ENCODE.

  PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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  GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

  tissues encode rt-pcr comparative automated

• Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

  PMID 18719945 · PMC2716558 · Human genetics · 2008 · 8 claims · 6 setups

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  PCDH15 has an updated gene structure with four additional exons beyond the previously reported 35, producing isoforms in four classes with three alternative cytoplasmic domains (CD1, CD2, CD3).

  genomic retina cdna protocadherin str pcr rt-pcr

• Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

  PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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  Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

  c57bl orthologous alpha-defensin defensin manual comparative sequence

• From the gamma-glutamyl cycle to the glycan cycle: a road with many turns and pleasant surprises.

  PMID 19840938 · PMC2787308 · The Journal of biological chemistry · 2009 · 8 claims · 8 setups

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  γ-Glutamyl transpeptidase (GGT) activity in rat liver shows biphasic changes during azo dye-induced hepatocarcinogenesis, mirroring the oncofetal expression pattern of α-fetoprotein

  liver tissues ascites hepatoma spectrophotometric enzyme glycan

• Proteomic and genetic approaches identify Syk as an AML target.

  PMID 19800574 · PMC2803063 · Cancer cell · 2009 · 8 claims · 8 setups

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  EGFR inhibitors (e.g., gefitinib) induce AML differentiation through a non-EGFR, off-target mechanism

  hl-60 aml molm-14 luciferase-labeled phospho-tyrosine kinome-wide secondary