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Status |
Public on May 17, 2011 |
Title |
genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 191 |
Sample type |
genomic |
|
|
Channel 1 |
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 |
Cy5
|
Label protocol |
amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
|
|
|
Channel 2 |
Source name |
red sector arising after re-replication at ChrIV567 in rad52 background
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
strain: YJL7644 sector induction: re-replication at ChrIV567 in rad52 background sample type: red sector arising after re-replication at ChrIV567 in rad52 background
|
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 6
|
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.
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|
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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 |
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