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List of the digital codes of experiments

  • 1. Footprinting reactions:
    • 1.1.DNAase I:
      • 1.1.1. with crude nuclear extract
      • 1.1.2. with mutated oligonucleotides
      • 1.1.3. comparison between fragments of different genes
      • 1.1.4. in the presence of increasing amounts of a competitor oligonucleotide
      • 1.1.5. in the presence of pure protein
      • 1.1.6. in the presence of crude nuclear extract and antibodies for transcription factor
    • 1.2. methidiumpropyl-EDTA.Fe(II)
    • 1.3. DNAse II footprint
    • 1.4. hydroxyl radicals
    • 1.5. footprinting in vivo
    • 1.6. ortophenantroline cooper footprint (OPCU)
  • 2. Exonuclease digests
    • 2.1. exonuclease III
    • 2.2. alpha exonuclease
  • 3. Electrophoretic mobility shift assays (EMSA):
    • 3.1. with crude nuclear extract
    • 3.2. using oligonucleotides for comparison or competition
      • 3.2.1. corresponding to the binding sites of the same type from different genes
      • 3.2.2. corresponding to binding sites of different types
      • 3.2.3  corresponding to binding sites and flanking sequences
    • 3.3. with oligonucleotides carrying point mutations
    • 3.4. cross-competition experiments
    • 3.5. with purified or recombinant protein or with the extracts from cells producing recombinant transcription factor
      • 3.5.1. gel mobility shift assay with extracts enriched with transcription factor
      • 3.5.2. gel mobility shift assay with extracts deprived with transcription factor
    • 3.6. with crude nuclear extract and antibodies (supershift).
      3.7. identification of transcription factor from DNA-protein complex corresponding to EMSA band
  • 4. DNA modification reactions
    • 4.1. methylation protection
    • 4.2. methylation interference
    • 4.3. ethylation protection
    • 4.4. ethylation interference
    • 4.5. demethylation
  • 5. Primer extension assay
    • 5.2 RACE ( rapid  amplification cDNA 5'end)
    • 5.5 RNase protection analysis
    • 5.6 S1 nuclease protection
  • 6. Transient expression analysis and experiments on transgenic organisms or cells.
    • 6.1. Analysis of deletions mutants:
      • 6.1.1. deletion size is more than 30 b.p.
      • 6.1.2. deletion size is up to 30 b.p.
      • 6.1.3. an effect of insertions
    • 6.2. An effect of point mutations on the expression
    • 6.3. Conferring of sequence to a geterologous or homologous promoters
      • 6.3.1. Conferring of the regions more than 30 b.p.
      • 6.3.2. Conferring of the separate site (up to 30 b.p.)
      • 6.3.3 Conferring of the region in direct and indirect orientations
    • 6.4. Tandem repeats of the binding site.
    • 6.5. Analysis of inducer (repressor) influence on the gene expression
    • 6.6. analysis of a reporter gene expression in the presence of purified transcription factors or vectors expressing transcription factors of given types.
      • 6.6.1. influence of purified or recombinant transcription factor on the reporter gene expression in vitro
      • 6.6.1.1. wild type (intact) transcription factor
      • 6.6.1.2. modified transcription factor (fusion proteins, truncated proteins, with mutations, deletions, killer-factors etc.)
      • 6.6.2. (in vivo) cotransfection assay
      • 6.6.2.1. wild type (intact) transcription factor
      • 6.6.2.2. modified transcription factor (fusion proteins, truncated proteins, with mutations, deletions, killer-factors etc.)
      • 6.6.3 analysis of a reporter gene expression in vitro using extracts deprived with transcription factor
      • 6.6.3.2 analysis of a reporter gene expression in vivo using cells without transcription factor
      • 6.3.3.3 analysis of a reporter gene expression in vivo using cells deprived with transcription factor (in the presence of  antibodies, oligonucleotides carrying binding site, etc)
    • 6.7. Transcription competition assay.
      • 6.7.1. In the presence of oligonucleotides carrying intact (wild type) binding site
      • 6.7.2. In the presence of oligonucleotides carrying mutated binding site.
    • 6.8. expression of the reporter gene by plasmid constructions containing regulatory region or unit being investigated.
    •  
  • 7. Homology of the binding site:
    • 7.1. with consensus of fixed type
    • 7.2. with the binding site from regulatory region of the homologous gene
    • 7.3. with the binding site of the same type from regulatory region of dissimilar gene
  • 8. ABCD-assay (avidin-biotin complex DNA-binding assay) 
  • 9. Filter binding assay
    • 9.2. using for comparison oligonucleotides corresponding to binding sites of different types
    • 9.3. with oligonucleotides carrying point mutations
    • 9.5. In situ binding of cloned transcription factors to synthetic oligonucleotides
  • 10. DNA-cellulose competition binding assay
  • 11.1  Protein- DNA immunoprecipitation assay (immunoselection)
  • 11.2  Chromatin immunoprecipitation
  • 12. In situ mutagenesis

revised October , 2003

 

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