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Sample GSM1336032 Query DataSets for GSM1336032
Status Public on Mar 15, 2014
Title MC2Ao-317(+167to-106)HMRE-E-YJL8538_2-rerep3hr
Sample type genomic
 
Channel 1
Source name YJL8538 M phase + Induced 3hr
Organism Saccharomyces cerevisiae
Characteristics strain: YJL8538
phase: re-replicating (M phase + Induced 3hr)
genotype: MC2Ao-317(+167to-106)HMRE-E
Growth protocol Cells grown as described in Richardson CD and Li JJ PLoS Genetics 2014. Ch1 samples taken from replicating (S phase) or re-replicating (M phase + 3/6 hour induced). Ch2 samples taken from M phase arrested DNA.
Extracted molecule genomic DNA
Extraction protocol DNA was purified by organic extraction and ethanol precipitation, or by more extensive methods when large quantities were needed. See Richardson CD and Li JJ PloS Genetics 2014.
Label Cy5
Label protocol Amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
 
Channel 2
Source name YJL7695 M phase arrested DNA
Organism Saccharomyces cerevisiae
Characteristics strain: YJL7695
phase: M phase arrested
sample type: Non-rereplicating reference DNA
Growth protocol Cells grown as described in Richardson CD and Li JJ PLoS Genetics 2014. Ch1 samples taken from replicating (S phase) or re-replicating (M phase + 3/6 hour induced). Ch2 samples taken from M phase arrested DNA.
Extracted molecule genomic DNA
Extraction protocol DNA was purified by organic extraction and ethanol precipitation, or by more extensive methods when large quantities were needed. See Richardson CD and Li JJ PloS Genetics 2014.
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 63C for 18-48
Scan protocol Arrays were scanned with an Axon 3000B scanner using GenePixPro6.0.
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; (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 2. VALUE is the log2 of the normalized ratio of Cy5 to Cy3; note that to convert to usable copy number profiles raise two to the indicated value.
 
Submission date Feb 27, 2014
Last update date Mar 15, 2014
Contact name Chris Richardson
E-mail(s) [email protected]
Organization name UCSB
Department Molecular, Cellular, and Developmental Biology
Street address UCSB
City Santa Barbara
State/province CA
ZIP/Postal code 93106-9625
Country USA
 
Platform ID GPL3412
Series (1)
GSE55420 Regulatory Mechanisms That Prevent Re-initiation of DNA Replication Can Be Locally Modulated at Origins by Nearby Sequence Elements

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 4.28408E-06
15S_rRNA1 1.033951616
15S_rRNA2 0.008937409
21S_rRNA_3
21S_rRNA_4 0.011902867
21S_rRNA0
21S_rRNA1 -0.177782835
21S_rRNA2 -0.092507855
9S_rRNA
9S_rRNA_5 -0.756003758
CEN1 0.680314661
CEN10
CEN11
CEN12 1.025172512
CEN13
CEN14 0.858911965
CEN15
CEN16
CEN2
CEN3

Total number of rows: 13678

Table truncated, full table size 245 Kbytes.




Supplementary file Size Download File type/resource
GSM1336032_MC2Ao-317_+167to-106_HMRE-E-YJL8538_2-rerep3hr.gpr.gz 1.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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