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Status |
Public on Feb 04, 2008 |
Title |
YAP6-TAP 4.7mM MMS treatment replicate 1 |
Sample type |
genomic |
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Channel 1 |
Source name |
YAP6-TAP, 4.7mM MMS, input DNA
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
Yeast BY4741 strain with YAP6-TAP
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were fixed with 1% formaldehyde, lysed, and sonicated to shear DNA. DNA fragments bound by the tagged TF were enriched by immunoprecipitation with an anti-TAP antibody (Open Biosystems). Afer reversal of crosslinking, DNA fragments were purified by phenol chloroform extraction
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Label |
Cy3
|
Label protocol |
non-antibody enriched DNA sample was amplified by LM-PCR using a Cy3 label.
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|
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Channel 2 |
Source name |
YAP6-TAP, 4.7mM MMS, anti-TAP enriched
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
Yeast BY4741 strain with YAP6-TAP
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were fixed with 1% formaldehyde, lysed, and sonicated to shear DNA. DNA fragments bound by the tagged TF were enriched by immunoprecipitation with an anti-TAP antibody (Open Biosystems). Afer reversal of crosslinking, DNA fragments were purified by phenol chloroform extraction
|
Label |
Cy5
|
Label protocol |
Enriched DNA was amplified and Cy5-labeled by ligation-mediated PCR (LM-PCR).
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Hybridization protocol |
Cy-3 and Cy-5 labeled samples were mixed with hybridization buffer (Agilent In Situ Hybridization Kit) and co-hybridized to the Yeast Whole Genome Tiling Array (G4486A, Agilent Technologies). Slides were hybridized for 17h at 60 degree Celcius in a rotating oven, and washed
|
Scan protocol |
Scanned on an GenePix 4000A scanner (Axon Instruments) at a 10.0 um resolution Images were quantified using GenePix Pro 6.0 software (Axon Instruments)
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Description |
yeast cells treated with 4.7mM MMS, enriched DNA compared to input genomic DNA.
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Data processing |
Background subtraction. Background-adjusted log ratios were then corrected for cyanine-dye dependent bias using Loess normalization
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Submission date |
Jan 10, 2008 |
Last update date |
Feb 04, 2008 |
Contact name |
Kai Tan |
Organization name |
University of California San Diego
|
Department |
Bioengineering
|
Street address |
9500 Gilman Drive
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92093 |
Country |
USA |
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Platform ID |
GPL3737 |
Series (1) |
GSE10146 |
A systems approach to delineate functions of YAP family members |
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