|
| Status |
Public on Oct 06, 2017 |
| Title |
ORC4 (BY-rDNA) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ssDNA in ORC4 (BY-rDNA) G1 phase
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ORC4 (BY-rDNA)
phase: G1 phase
|
| Treatment protocol |
Alpha factor arrested cells were synchronously released into S phase by addition of pronase (0.3 mg/ml) into media containing 200 mM Hydroxyurea. Cells were collected at 30 min post release.
|
| Growth protocol |
Early log phase (OD660 ~0.25) cells were arrested in G1 by the addition of alpha-factor at a final concentration 3 μM.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part I. Sample collection and Preparation of Yeast DNA Embedded in Agarose Plugs)
|
| Label |
Cy5
|
| Label protocol |
ssDNA labeling was performed as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part II. Random-primed in-gel labeling of ssDNA by Klenow)
|
| |
|
| Channel 2 |
| Source name |
ssDNA in ORC4 (BY-rDNA) +HU 30 min
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ORC4 (BY-rDNA)
phase: S phase
|
| Treatment protocol |
Alpha factor arrested cells were synchronously released into S phase by addition of pronase (0.3 mg/ml) into media containing 200 mM Hydroxyurea. Cells were collected at 30 min post release.
|
| Growth protocol |
Early log phase (OD660 ~0.25) cells were arrested in G1 by the addition of alpha-factor at a final concentration 3 μM.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part I. Sample collection and Preparation of Yeast DNA Embedded in Agarose Plugs)
|
| Label |
Cy3
|
| Label protocol |
ssDNA labeling was performed as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part II. Random-primed in-gel labeling of ssDNA by Klenow)
|
| |
|
| |
| Hybridization protocol |
Microarray hybridization was performed as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part III. Agilent microarray hybridization and scanning)
|
| Scan protocol |
Microarray scanning was performed as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part III. Agilent microarray hybridization and scanning)
|
| Data processing |
(Extraction Software: Agilent Feature Extractor) (Extraction Software Version: 10.5.1.1) (Datafile type: Agilent result file)
Background subtracted median values from the two channels were used to calculate the ratio of Cy3:Cy5 as the raw ratio of ssDNA (S/G1). The raw normalized ratios of ssDNA for all genomic locations were then smoothed over a 22 kb window by loess smoothing.
|
| |
|
| Submission date |
Oct 05, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Joseph Sanchez |
| Organization name |
University of Washington
|
| Department |
Molecular and Cellular Biology
|
| Lab |
Brewer/Raghuraman
|
| Street address |
Foege Building S-250, 3720 15th Ave NE
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
| |
|
| Platform ID |
GPL10930 |
| Series (1) |
| GSE104671 |
Single stranded DNA formation during S phase in orc4Y232C yeast cells |
|
