|
Status |
Public on Mar 17, 2006 |
Title |
A364a_S_phase_LiUP1_202_RME7-21_wtrerep_135mN1_35 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
S phase DNA A364a
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
YJL5834 135 minutes after release from G1 (alpha factor) into 0.1M hydroxyurea
|
Extracted molecule |
genomic DNA |
Label |
Cy5
|
Label protocol |
amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
|
|
|
Channel 2 |
Source name |
G1 phase DNA A364a
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
YJL5834 arrested in G1 (alpha factor)
|
Extracted molecule |
genomic DNA |
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 24 hours.
|
Scan protocol |
Arrays were scanned with an Axon 3000B scanner using GenePix4.0.
|
Description |
Data from Figure 1D of MBoC paper (citation coming soon)
|
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 the DNA content of the replicating cells as determined by flow cytometry. The DNA content was 1.35C.
|
|
|
Submission date |
Feb 02, 2006 |
Last update date |
Mar 17, 2006 |
Contact name |
Joachim J Li |
E-mail(s) |
[email protected]
|
Phone |
415-476-8782
|
Fax |
415-514-4080
|
Organization name |
University of California, San Francisco
|
Department |
Microbiology and Immunology
|
Lab |
Li
|
Street address |
600 16th Street S376
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94143-2200 |
Country |
USA |
|
|
Platform ID |
GPL3412 |
Series (1) |
GSE4181 |
Genome-wide mapping of DNA re-replication in S. cerevisiae |
|
Data table header descriptions |
ID_REF |
|
PRE_VALUE |
Cy5/Cy3 ratio normalized to DNA content determined by flow cytometry (NOT a log value) |
VALUE |
log2 of PRE_VALUE |
Median of Ratios (635/532) |
GenePix raw Cy5/Cy3 ratio |
Rgn R^2 (635/532) |
GenePix coefficient of determination for the current regression value for wavelengths 1 and 2 |
GenePix Flags |
GenePix flag used to mark the quality of a feature (0 = Good, <0 = Bad) |
Dia. |
GenePix diameter in �m of the feature-indicator |
F635 Median |
GenePix median feature pixel intensity at wavelength 635 |
F635 Mean |
GenePix mean feature pixel intensity at wavelength 635 |
F635 SD |
GenePix standard deviation of the feature pixel intensity at wavelength 635 |
B635 Median |
GenePix median background intensity at wavelength 635 |
B635 Mean |
GenePix mean background intensity at wavelength 635 |
B635 SD |
GenePix standard deviation of the local background intensity at wavelength 635 |
% > B635+1SD |
GenePix percentage of feature pixels with intensities more than one standard deviation above the background intensity, at wavelength 635 |
% > B635+2SD |
GenePix percentage of feature pixels with intensities more than two standard deviations above the background intensity, at wavelength 635 |
F635 % Sat. |
GenePix percentage of feature pixels at wavelength 635 that are saturated |
F532 Median |
GenePix median feature pixel intensity at wavelength 532 |
F532 Mean |
GenePix mean feature pixel intensity at wavelength 532 |
F532 SD |
GenePix standard deviation of the feature pixel intensity at wavelength 532 |
B532 Median |
GenePix median background intensity at wavelength 532 |
B532 Mean |
GenePix mean background intensity at wavelength 532 |
B532 SD |
GenePix standard deviation of the local background intensity at wavelength 532 |
% > B532+1SD |
GenePix percentage of feature pixels with intensities more than one standard deviation above the background intensity, at wavelength 532 |
% > B532+2SD |
GenePix percentage of feature pixels with intensities more than two standard deviations above the background intensity, at wavelength 532 |
F532 % Sat. |
GenePix percentage of feature pixels at wavelength 532 that are saturated |
Ratio of Medians (635/532) |
GenePix ratio of the median intensities of each feature for wavelengths 635 and 532, with the median background intensity subtracted |
Ratio of Means (635/532) |
GenePix ratio of the arithmetic mean intensities of each feature for wavelengths 635 and 532, with the median background intensity subtracted |
Mean of Ratios (635/532) |
GenePix geometric mean of the pixel-by-pixel ratios of pixel intensities for wavelengths 635 and 532, with the median background intensity subtracted |
Ratios SD (635/532) |
GenePix standard deviation of the log of pixel intensity ratios for wavelengths 635 and 532 |
Rgn Ratio (635/532) |
GenePix regression ratio for wavelengths 635 and 532 (slope of the line of best fit (chi-square or minimum-of-squares method) through the set of pixels in a circle of diameter twice that of the feature-indicator of the current feature) |
F Pixels |
GenePix total number of feature pixels |
B Pixels |
GenePix total number of local background pixels |
Sum of Medians |
GenePix sum of the median intensities for each wavelength, with the median background intensity at each wavelength subtracted |
Sum of Means |
GenePix sum of the arithmetic mean intensities for each wavelength, with the median background intensity at each wavelength subtracted |
Log Ratio (635/532) |
GenePix log2 transform of the ratio of the medians for wavelengths 635 and 532 |
F635 Median - B635 |
GenePix median feature pixel intensity at wavelength 635 with the median background intensity subtracted |
F532 Median - B532 |
GenePix median feature pixel intensity at wavelength 532 with the median background intensity subtracted |
F635 Mean - B635 |
GenePix mean feature pixel intensity at wavelength 635 with the median background intensity subtracted |
F532 Mean - B532 |
GenePix mean feature pixel intensity at wavelength 635 with the median background intensity subtracted |