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| Status |
Public on Dec 04, 2008 |
| Title |
DIP-chip from Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5 |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
DNA Immunoprecipitation was performed using purified, naked, genomic DNA and purified recombinant DNA binding domains for S. cerevisiae transcription factors (Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5) and then competitively hybridized against input DNA on NimbleGen 385k whole-genome, 32bp, tiling arrays to identify the consensus sequence for each transcription factor as a whole in the genome.
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| Overall design |
Each protein was used for 2 independent replicates at a protein concentration of 40nM. The second replicate is a dye-swap. During analysis, regions of the genome had to be identified as bound in both replicates as well as the average of the two replicates to be considered true binding sites.
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| Contributor(s) |
Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Yeo AL, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR |
| Citation(s) |
19092803 |
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| Submission date |
Nov 26, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Jason D Lieb |
| E-mail(s) |
jlieb@bio.unc.edu
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| Phone |
919-843-3228
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| URL |
http://www.bio.unc.edu/faculty/lieb/labpages/default.shtml
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Biology
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| Lab |
Jason Lieb
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| Street address |
203 Fordham Hall
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platforms (1) |
| GPL7699 |
NimbleGen 385k S. cerevisiae 32bp tiling array |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA109407 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE13751_RAW.tar |
432.9 Mb |
(http)(custom) |
TAR (of GFF, PAIR, TIFF) |
| Processed data included within Sample table |
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