|
| Status |
Public on May 17, 2011 |
| Title |
genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 82 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
red sector arising after negative control non-re-replication at ChrIV567
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YJL7554
sector induction: negative control non-re-replication at ChrIV567
sample type: red sector arising after negative control non-re-replication at ChrIV567
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
see BM Green et al. 2006
|
| Label |
Cy5
|
| Label protocol |
amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
|
| |
|
| Channel 2 |
| Source name |
negative control MC2A strain in G2/M
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YJL6558
sector induction: n/a
sample type: negative control MC2A strain in G2/M
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
see BM Green et al. 2006
|
| Label |
Cy3
|
| Label protocol |
amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 16 to 24 hours
|
| Scan protocol |
Arrays were scanned with an Axon 3000B scanner using GenePix4.0.
|
| Description |
Supp Table 4
|
| Data processing |
Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.
Value is the log2 of the normalized ratio of Cy5 to Cy3 – note that to convert to usable replication profiles, raise two to the indicated value.
|
| |
|
| Submission date |
May 26, 2010 |
| Last update date |
May 17, 2011 |
| Contact name |
Brian M Green |
| Organization name |
University of California, San Francisco
|
| Department |
Department of Biochemistry
|
| Lab |
Joachim Li
|
| Street address |
600 16th Street, S376 Genentech Hall
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL3412 |
| Series (1) |
| GSE22018 |
Loss of DNA replication control is a potent initiator of gene amplification |
|
