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).

• Methods for proteomic analysis of transcription factors.

  PMID 19726046 · PMC2778203 · Journal of chromatography. A · 2009 · 8 claims · 8 setups

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  Systematic oligonucleotide 'trapping' at nM DNA concentrations allows purification of TF-RE complexes in a highly purified state, exploiting the high specific affinity vs. low non-specific affinity of TFs for DNA

  nuclear crude intact partially emsa southwestern systematic

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

  PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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  A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

  primate hepg2 32p-labeled sequence rt-pcr luciferase

• Functional analysis of human mutations in homeodomain transcription factor PITX3.

  PMID 17888164 · PMC2093940 · BMC molecular biology · 2007 · 7 claims · 5 setups

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  Both S13N and G219fs mutants show partial loss-of-function in DNA-binding and/or transactivation activity, with G219fs more severely affected than S13N

  lens western immunocytochemistry electrophoretic

• Rare-type mutations of MMAC1 tumor suppressor gene in human glioma cell lines and their tumors of origin.

  PMID 10551321 · PMC5926156 · Japanese journal of cancer research : Gann · 1999 · 8 claims · 6 setups

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  6 of 10 glioma cell lines examined showed MMAC1 mutations with presumed loss of heterozygosity (LOH)

  glioma pcr northern rt-pcr sscp

• The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

  PMID 17438525 · PMC2669504 · Molecular vision · 2007 · 8 claims · 8 setups

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  NR2E3 LBD fused to a heterologous Gal4 DBD mediates dose-dependent transcriptional repression on Gal4-responsive reporters.

  cos-1 hela luciferase western electrophoretic

• Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

  PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

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  Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

  tumor promoter hela cdna bead tag-microarray

• Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

  PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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  PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

  rt4d6 gst-sox10 microarray comparative real

• Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

  PMID 18160415 · PMC2275099 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  HMGB1 is a novel HNF1α-interacting protein identified via a co-IP-MS screening strategy

  hepg2 recombinant co-immunoprecipitation immunofluorescence gst