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| Status |
Public on Feb 15, 2021 |
| Title |
Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome variation profiling by array
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| Summary |
We mapped ssDNA formation in WT and rad53K227A cells in both A364a and W303 background.
We also performed whole genome sequencing of the A364a strain.
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| Overall design |
Briefly, cell cultures were grown to an OD600 of 0.25~0.3 in YPD medium, followed by G1 arrest with 200 nM α-factor. Pronase (0.02 mg/mL) was used to synchronously release cells into S phase in the presence of 200 mM hydroxyurea (HU). G1 control and S phase samples were collected prior to cell cycle release and after 1 h treatment of HU, respectively. Three-hundred ml of cells from each sample were collected and spheroplasted in agarose plugs for ssDNA labeling. Differentially labeled G1 (Cy5-dUTP) and S phase (Cy3-dUTP) DNA were co-hybridized onto Agilent Yeast Whole Genome ChIP-to-chip 4 × 44K (G4493A) microarrays and the data were extracted by the Agilent Feature Extraction Software (v9.5.1). The relative quantity of ssDNA at a given genomic locus was calculated as the ratio of the fluorescent signal from the S phase sample to that of the G1 control, followed by Loess-smoothing over a 6-kb window at a step size of 250 bp.
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| Contributor(s) |
Peng J, Feng W |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Feb 14, 2021 |
| Last update date |
Feb 17, 2021 |
| Contact name |
Wenyi Feng |
| E-mail(s) |
[email protected]
|
| Phone |
3154648701
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| Organization name |
SUNY Upstate Medical University
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| Department |
Biochemistry and Molecular Biology
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| Lab |
Wenyi Feng
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| Street address |
750 East Adams Street
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| City |
Syracuse |
| State/province |
NY |
| ZIP/Postal code |
13210 |
| Country |
USA |
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| Platforms (1) |
| GPL10930 |
Agilent-014810 Yeast Whole Genome ChIP-on-Chip Microarray 4x44K (G4493A) [Probe Name version] |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA701815 |
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