|
| Status |
Public on Aug 31, 2010 |
| Title |
YJB9929s_rep1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
G1-phase cells, YJB9929s
|
| Organism |
Candida albicans |
| Characteristics |
strain: YJB9929s
|
| Treatment protocol |
G1- and S-phase cells were sorted by FACS.
|
| Growth protocol |
Cells were grown in YPAD (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 rounds 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, YJB9929s
|
| Organism |
Candida albicans |
| Characteristics |
strain: YJB9929s
|
| Treatment protocol |
G1- and S-phase cells were sorted by FACS.
|
| Growth protocol |
Cells were grown in YPAD (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 rounds 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 |
Standard Agilent protocol.
|
| Scan protocol |
Agilent, 5micron, 100%PMT.
|
| Description |
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.
The raw data for this Sample is in the rows with a '1' in the 'Block' column of the linked .srr file.
The fully processed replication timing data is available in the 'GSE17963_final_data.txt' file, which is linked to the Series GSE17963 record as a supplementary file.
|
| |
|
| Submission date |
Sep 03, 2009 |
| Last update date |
Aug 31, 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 |
GPL9148 |
| Series (1) |
| GSE17963 |
Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase |
|
