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| Status |
Public on Jul 17, 2016 |
| Title |
CLAMP Protein Binding Microarray (PBM) experiment |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by array
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| Summary |
To investigate the DNA binding specificity of the CLAMP protein, we have designed a custom PBM to interrogate the binding of CLAMP to DNA sequences extracted from the Drosophila melanogaster genome. Specific regions were extracted based on ChIP-seq data, motif occurence and proximity to gene transcription start sites.
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| Overall design |
N-terminal GST-tagged protein samples were made for the C-terminal four and six zinc finger portions of the protein CLAMP; samples were made by in vitro transcription translation (IVT). IVT reaction mixtures for the two CLAMP constructs were applied directly to the PBM microarray and incubated for 1hour. Microarray-bound protein was fluorescently labeled using Alexa488-conjugated antibodies targeting GST, and the microarray was scanned in using a standard microarray scanner. Median fluorescence intensity over eight replicate probes was reported for each unique DNA sequence on the microarray.
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| Contributor(s) |
Siggers T |
| Citation(s) |
27414415 |
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| Submission date |
Jun 16, 2016 |
| Last update date |
Feb 15, 2018 |
| Contact name |
Michael Tolstorukov |
| E-mail(s) |
tolstorukov@molbio.mgh.harvard.edu
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| Organization name |
Massachusetts General Hospital
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| Department |
Molecular Biology
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| Street address |
185 Cambridge Street
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platforms (1) |
| GPL22023 |
Agilent-037964 mre_4x180k_design_1_1211 Protein Binding Microarray (Condensed probe version) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE83444 |
Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation |
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| Relations |
| BioProject |
PRJNA325941 |
