|
Status |
Public on Feb 17, 2023 |
Title |
35 rDNA strain, 40 min S phase |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
40 min S phase, HH (unreplicated) DNA, 35 copies rDNA
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
cell cycle phase: S phase s phase time: 40 min fraction: HH (unreplicated) DNA
|
Treatment protocol |
Cells were released into S phase by addition of Pronase. We collected samples at intervals through the ensuing S phase (30,35,40,45,50 min for 35 rDNA strain; 25,30,35,40,45,55 min for 180 rDNA strain).
|
Growth protocol |
We grew cells in isotopically dense (13C-glucose, 15N-ammonium sulfate) for ≥7 population doublings. We then arrested the cells in G1 using a-factor, filtered and resuspended the cells in isotopically light (12C, 14N) medium.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted using glass beads and phenol/chloroform (standard smash-and-grab method). The DNA was digested with EcoRI. Heavy-heavy (HH) and heavy-light (HL) DNA were separated by ultracentrifugation in cesium chloride gradients. The gradients were drip-fractionated. HH and HL portions of the gradient were identified by slot blot hybridization. The DNA was recovered from CsCl by ethanol precipitation.
|
Label |
Cy3
|
Label protocol |
200 ng of HH or HL DNA were labeled with Cy3 and Cy5, respectively, using random-primed synthesis with exonuclease-deficient Klenow.
|
|
|
Channel 2 |
Source name |
40 min S phase, HL (replicated) DNA, 35 copies rDNA
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
cell cycle phase: S phase s phase time: 40 min fraction: HL (replicated) DNA
|
Treatment protocol |
Cells were released into S phase by addition of Pronase. We collected samples at intervals through the ensuing S phase (30,35,40,45,50 min for 35 rDNA strain; 25,30,35,40,45,55 min for 180 rDNA strain).
|
Growth protocol |
We grew cells in isotopically dense (13C-glucose, 15N-ammonium sulfate) for ≥7 population doublings. We then arrested the cells in G1 using a-factor, filtered and resuspended the cells in isotopically light (12C, 14N) medium.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted using glass beads and phenol/chloroform (standard smash-and-grab method). The DNA was digested with EcoRI. Heavy-heavy (HH) and heavy-light (HL) DNA were separated by ultracentrifugation in cesium chloride gradients. The gradients were drip-fractionated. HH and HL portions of the gradient were identified by slot blot hybridization. The DNA was recovered from CsCl by ethanol precipitation.
|
Label |
Cy5
|
Label protocol |
200 ng of HH or HL DNA were labeled with Cy3 and Cy5, respectively, using random-primed synthesis with exonuclease-deficient Klenow.
|
|
|
|
Hybridization protocol |
Hybridization and washing were done using standard conditions specified by Agilent (using Agilent Blocking Agent and HI-rPM hybridization buffer).
|
Scan protocol |
Arrays were scanned on an Agilent Technologies Scanner G2505C and features were extracted using protocol CGH 105 Dec08 CP in feature extractor (FE) v. 10.7.3.1
|
Description |
HH and HL DNA were separated by CsCl density gradient centrifugation
|
Data processing |
After extraction of hybridization intensities, we used the known % replication values from the slot blot analysis to normalize the overall % replication in each sample, with an added correction for the percentage of cells in the population that successfully completed S phase (obtained from the maximum % replication seen at the end of S phase from the slot blot analysis).
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|
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Submission date |
May 30, 2022 |
Last update date |
Feb 19, 2023 |
Contact name |
Mosur K Raghuraman |
E-mail(s) |
[email protected]
|
Organization name |
University of Washington
|
Department |
Genome Sciences Box 355065
|
Lab |
Brewer/Raghuraman
|
Street address |
Foege Bldg, 3720 15th Ave NE
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
|
|
Platform ID |
GPL10930 |
Series (1) |
GSE205068 |
Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast |
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