|
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.
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|
|
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 |
|