|
| Status |
Public on Mar 15, 2014 |
| Title |
MC2Ao-RIP1238-ARS1238(27bp)-YJL10297-rerep6hr |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
YJL10297 M phase + Induced 6hr
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YJL10297
phase: re-replicating (M phase + Induced 6hr)
genotype: MC2Ao-RIP1238-ARS1238(27bp)
|
| 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 |
|
