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Sample GSM547540 Query DataSets for GSM547540
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.
 
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

Data table header descriptions
ID_REF
VALUE Value is the log2 of the normalized ratio of Cy5 to Cy3

Data table
ID_REF VALUE
15S_rRNA_2
15S_rRNA1
15S_rRNA2
21S_rRNA_3
21S_rRNA_4 0.060855318
21S_rRNA0
21S_rRNA1
21S_rRNA2
9S_rRNA
9S_rRNA_5 0.196353396
CEN1
CEN10
CEN11
CEN12
CEN13
CEN14 0.01860283
CEN15
CEN16
CEN2
CEN3

Total number of rows: 14062

Table truncated, full table size 210 Kbytes.




Supplementary file Size Download File type/resource
GSM547540_ST6_rad_YJL7644.gpr.gz 1.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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