|
| Status |
Public on Feb 04, 2008 |
| Title |
YAP4-TAP 7.1mM MMS treatment replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
YAP4-TAP, 7.1mM MMS, input DNA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Yeast BY4741 strain with YAP4-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 |
Cy3
|
| Label protocol |
non-antibody enriched DNA sample was amplified by LM-PCR using a Cy3 label.
|
| |
|
| Channel 2 |
| Source name |
YAP4-TAP, 7.1mM MMS, anti-TAP enriched
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Yeast BY4741 strain with YAP4-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).
|
| |
|
| |
| 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)
|
| Description |
yeast cells treated with 7.1mM MMS, enriched DNA compared to input genoimc DNA.
|
| Data processing |
Background subtraction. Background-adjusted log ratios were then corrected for cyanine-dye dependent bias using Loess normalization
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL3737 |
| Series (1) |
| GSE10146 |
A systems approach to delineate functions of YAP family members |
|
