|
| Status |
Public on Mar 04, 2010 |
| Title |
dpb3- rep2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
G1-phase cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
|
| Treatment protocol |
G1- and S- phase cells were sorted by FACS
|
| Growth protocol |
Cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) at 30º to log phase and fixated.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the MasterPure Yeast DNA purification kit (Epicentre)
|
| Label |
cy3
|
| Label protocol |
DNA was digested with DpnII and amplified by four ronds of random-octamer-primed Exo-Klenow DNA synthesis (Invitrogen BioPrime ArrayCGH amplification kit) with amino-allyl modified nucleotides and subsequently labeled with Cy dyes
|
| |
|
| Channel 2 |
| Source name |
S-phase cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
|
| Treatment protocol |
G1- and S- phase cells were sorted by FACS
|
| Growth protocol |
Cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) at 30º to log phase and fixated.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the MasterPure Yeast DNA purification kit (Epicentre)
|
| Label |
cy5
|
| Label protocol |
DNA was digested with DpnII and amplified by four ronds of random-octamer-primed Exo-Klenow DNA synthesis (Invitrogen BioPrime ArrayCGH amplification kit) with amino-allyl modified nucleotides and subsequently labeled with Cy dyes
|
| |
|
| |
| Hybridization protocol |
Agilent
|
| Scan protocol |
Agilent, 5micron, 100%PMT
|
| Description |
raw data column: Strains9 (block3)
S vs G1 Replication timing
|
| Data processing |
Images were analyzed with SpotReader (Niles Scientific). Weak (<2std above control probe mean) and saturated probe reads were removed from further analysis. Data was LOWESS-normalized.
|
| |
|
| Submission date |
Jul 15, 2009 |
| Last update date |
Mar 04, 2010 |
| Contact name |
Amnon Koren |
| E-mail(s) |
koren@genetics.med.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL4131 |
| Series (1) |
| GSE17120 |
MRC1-Dependent Scaling of the Budding Yeast DNA Replication Timing Program |
|
