|
| Status |
Public on Sep 17, 2010 |
| Title |
ScYap4K252R-1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
fraction: IP enriched
antibody: anti-TAP
antibody manufacturer: Open Biosystems
antibody cat#: CAB1001
|
| Growth protocol |
Cells were innoculated to OD600=0.2, grown to 0.8 and treated for one hour with 0.03% MMS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 20 minutes, inactivated with glycine and washed with TBS. Cells were lysed for 2 hours (Vibrax-VXR 2000) with glass beads and sonicated for 4 cycles of 20 seconds (+100 seconds rest) at power setting 2 (Misonex Sonicator 3000) on ice. Lysate was incubated with Dynabeads M-280 conjugated with anti-TAP antibody (Open Biosystems CAB1001) overnight. Cross-link reversal was performed overnight at 65C.
|
| Label |
Cy5
|
| Label protocol |
As recommended using Sigma WGA2 amplification and Invitrogen 18095011, Cy5 and Cy3
|
| |
|
| Channel 2 |
| Source name |
Yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
fraction: whole cell extract input
|
| Growth protocol |
Cells were innoculated to OD600=0.2, grown to 0.8 and treated for one hour with 0.03% MMS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 20 minutes, inactivated with glycine and washed with TBS. Cells were lysed for 2 hours (Vibrax-VXR 2000) with glass beads and sonicated for 4 cycles of 20 seconds (+100 seconds rest) at power setting 2 (Misonex Sonicator 3000) on ice. Lysate was incubated with Dynabeads M-280 conjugated with anti-TAP antibody (Open Biosystems CAB1001) overnight. Cross-link reversal was performed overnight at 65C.
|
| Label |
Cy3
|
| Label protocol |
As recommended using Sigma WGA2 amplification and Invitrogen 18095011, Cy5 and Cy3
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.
|
| Scan protocol |
Images were quantified using GenePix Pro 6.0
|
| Data processing |
Background subtraction and LOWESS normalization, Rosetta Error Model
|
| |
|
| Submission date |
Sep 16, 2010 |
| Last update date |
Sep 16, 2010 |
| Contact name |
Dwight Kuo |
| Organization name |
UCSD
|
| Department |
Bioengineering
|
| Lab |
Trey Ideker
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL10930 |
| Series (1) |
| GSE15818 |
Coeevolution of a transcriptional network by compensatory trans and cis mutations |
|
