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Sample GSM280328 Query DataSets for GSM280328
Status Public on Aug 20, 2008
Title C1 evolved M4 vs DsRED 2
Sample type RNA
 
Channel 1
Source Name DsRED
Organism(s) Saccharomyces cerevisiae
Characteristics DsRED
Growth protocol Chemostat Growth Conditions; Single colonies were used to inoculate overnight cultures in 2% glucose Delft minimal medium grown at 30oC. These cultures were then used to inoculate glucose-limited chemostat cultures. Chemostat vessels were inoculated with ~6x10^7 in 20ml total volume. To ensure the cells had reached steady-state, the cultures were harvested approximately 48 hours after inoculation.; Protocol Type = Growth Conditions; Performer: Katy,,Kao
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source Name M4
Organism(s) Saccharomyces cerevisiae
Characteristics M4
Growth protocol Chemostat Growth Conditions; Single colonies were used to inoculate overnight cultures in 2% glucose Delft minimal medium grown at 30oC. These cultures were then used to inoculate glucose-limited chemostat cultures. Chemostat vessels were inoculated with ~6x10^7 in 20ml total volume. To ensure the cells had reached steady-state, the cultures were harvested approximately 48 hours after inoculation.; Protocol Type = Growth Conditions; Performer: Katy,,Kao
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; The software Feature Extraction v 9.1.5 (Agilent Technology, Santa Clara, CA) was used extract data from the scanned images, and to normalize the data using the Spike-In controls.; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Katy,,Kao
Description Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78819.gif
Genotype: M4
Chemostat evolution experiment C1 under glucose-limited condition at 30C. Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Apr 08, 2008
Contact name Gavin Sherlock
E-mail(s) sherlock@genome.stanford.edu
Phone 650 498 6012
Fax 650 724 3701
URL http://genetics.stanford.edu/~sherlock/
Organization name Stanford University
Department Genetics
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL6720
Series (1)
GSE11071 C1 evolved adaptive clones M1-M5

Data table header descriptions
ID_REF
Background Pixel Correlation
Box Bottom
Box Left
Box Right
Box Top
Error Model Used (0|1)
Error of Log Ratio
Feature Is Found (Green) (0|1)
Feature Is Found (Red) (0|1)
Feature Is Green Background Non-uniformity Outlier (0|1)
Feature Is Green Background Population Outlier (0|1)
Feature Is Green Non-uniformity Outlier (0|1)
Feature Is Green Population Outlier (0|1)
Feature Is Red Background Non-uniformity Outlier (0|1)
Feature Is Red Background Population Outlier (0|1)
Feature Is Red Non-uniformity Outlier (0|1)
Feature Is Red Population Outlier (0|1)
Feature Is Used for Global Background (0|1)
Feature Is Used for Normalization (0|1)
Final Processed Green Intensity
Final Processed Red Intensity
GNumBGUsed
GProcessedSigError
Green Background (mean)
Green Background (median)
Green Background Intensity Used
Green Channel Saturated (0|1)
Green Intensity (mean)
Green Intensity (median)
Green Intensity Is Well Above Background (0|1)
Green Net Intensity
Green Net Intensity Is Positive and Significant (0|1)
Green Normalized Net Intensity
Green Surrogate Used
Manual Flag
Number of Green Background Pixels
Number of Green Inlier Pixels
Number of Green Outlier Pixels (high intensity)
Number of Green Outlier Pixels (low intensity)
Number of Green Saturated Pixels
Number of Red Background Pixels
Number of Red Inlier Pixels
Number of Red Outlier Pixels (high intensity)
Number of Red Outlier Pixels (low intensity)
Number of Red Saturated Pixels
RNumBGUsed
RProcessedSigError
Red Background (mean)
Red Background (median)
Red Background Intensity Used
Red Channel Saturated (0|1)
Red Intensity (mean)
Red Intensity (median)
Red Intensity Is Well Above Background (0|1)
Red Net Intensity
Red Net Intensity Is Positive and Significant (0|1)
Red Normalized Net Intensity
Red Surrogate Used
Red-Green Net Pixel Correlation
Red-Green Normalized Net Pixel Correlation
Red-Green Pixel Correlation
Standard Deviation of Green Background Inlier Pixels
Standard Deviation of Green Inlier Pixels
Standard Deviation of Red Background Inlier Pixels
Standard Deviation of Red Inlier Pixels
Std Dev of Green Background Intensity
Std Dev of Red Background Intensity
Std Err of Green Net Intensity
Std Err of Green Normalized Net Intensity
Std Err of Red Net Intensity
Std Err of Red Normalized Net Intensity
X coordinate
Y coordinate
log(base 10) (P-value of Green Difference from Background)
log(base 10) (P-value of Log Ratio)
log(base 10) (P-value of Red Difference from Background)
log(base 10) (REDsignal/GREENsignal)
VALUE log(base 2) (REDsignal/GREENsignal)

Data table
ID_REF Background Pixel Correlation Box Bottom Box Left Box Right Box Top Error Model Used (0|1) Error of Log Ratio Feature Is Found (Green) (0|1) Feature Is Found (Red) (0|1) Feature Is Green Background Non-uniformity Outlier (0|1) Feature Is Green Background Population Outlier (0|1) Feature Is Green Non-uniformity Outlier (0|1) Feature Is Green Population Outlier (0|1) Feature Is Red Background Non-uniformity Outlier (0|1) Feature Is Red Background Population Outlier (0|1) Feature Is Red Non-uniformity Outlier (0|1) Feature Is Red Population Outlier (0|1) Feature Is Used for Global Background (0|1) Feature Is Used for Normalization (0|1) Final Processed Green Intensity Final Processed Red Intensity GNumBGUsed GProcessedSigError Green Background (mean) Green Background (median) Green Background Intensity Used Green Channel Saturated (0|1) Green Intensity (mean) Green Intensity (median) Green Intensity Is Well Above Background (0|1) Green Net Intensity Green Net Intensity Is Positive and Significant (0|1) Green Normalized Net Intensity Green Surrogate Used Manual Flag Number of Green Background Pixels Number of Green Inlier Pixels Number of Green Outlier Pixels (high intensity) Number of Green Outlier Pixels (low intensity) Number of Green Saturated Pixels Number of Red Background Pixels Number of Red Inlier Pixels Number of Red Outlier Pixels (high intensity) Number of Red Outlier Pixels (low intensity) Number of Red Saturated Pixels RNumBGUsed RProcessedSigError Red Background (mean) Red Background (median) Red Background Intensity Used Red Channel Saturated (0|1) Red Intensity (mean) Red Intensity (median) Red Intensity Is Well Above Background (0|1) Red Net Intensity Red Net Intensity Is Positive and Significant (0|1) Red Normalized Net Intensity Red Surrogate Used Red-Green Net Pixel Correlation Red-Green Normalized Net Pixel Correlation Red-Green Pixel Correlation Standard Deviation of Green Background Inlier Pixels Standard Deviation of Green Inlier Pixels Standard Deviation of Red Background Inlier Pixels Standard Deviation of Red Inlier Pixels Std Dev of Green Background Intensity Std Dev of Red Background Intensity Std Err of Green Net Intensity Std Err of Green Normalized Net Intensity Std Err of Red Net Intensity Std Err of Red Normalized Net Intensity X coordinate Y coordinate log(base 10) (P-value of Green Difference from Background) log(base 10) (P-value of Log Ratio) log(base 10) (P-value of Red Difference from Background) log(base 10) (REDsignal/GREENsignal) VALUE
1 .0253586 2646 6697 6697 2646 1 .1099049828 1 1 0 0 0 0 0 0 0 0 0 0 2159.32 20480.74 1 215.9646 40.81098 40 111.818 0 11340.71 10402 1 11228.9 1 2159.32 0 0 783 34 1 0 0 783 34 0 0 0 1 2049.612 50.17497 50 169.161 0 7376.706 6563.5 1 7207.54 1 20480.7 0 0 0 .772809 5.400818 2364.566 7.758094 2239.382 5.40082 7.75809 1123.06 215.965 721.296 2049.61 6697.56 2646.52 -148.47739407733 -18.212941073409 -127.519261700046 .9770284599 3.246
2 .0937541 2647 6722 6722 2647 1 .6231240535 0 0 0 0 0 0 0 0 0 0 0 0 14.3768 21.74768 1 14.08641 41.49128 41 110.975 0 76.48718 77 0 -34.4877 0 14.3768 24.068 0 688 39 0 0 0 688 39 0 0 0 1 21.31837 51.15552 50 168.054 0 105 106 0 -63.0542 0 21.7477 28.5013 0 0 .00231454 5.515883 7.996288 8.273734 19.90636 5.51588 8.27373 19.5017 14.0864 27.9386 21.3184 6722.63 2647 -4.69392683986687 0 -6.80538299360244 0 0
3 .0787212 2646 6748 6748 2646 1 .6228777758 1 1 0 0 0 0 0 0 0 0 0 0 14.44381 21.79555 1 14.15206 42.05526 42 110.141 0 76.83871 77 0 -33.3019 0 14.4438 24.2334 0 742 31 1 0 0 742 31 1 0 0 1 21.36529 50.78706 50 167.034 0 111.2258 111 0 -55.8082 0 21.7955 28.5013 0 0 .164887 5.697116 15.1065 7.383495 12.67467 5.69712 7.3835 19.5017 14.1521 27.9386 21.3653 6748.48 2646.51 -4.44747413902118 0 -5.66606932560334 0 0
4 .0800817 2647 6773 6773 2647 1 .2937945267 1 1 0 0 0 0 0 0 0 0 0 0 113.7447 53.61384 1 12.7587 44.10638 43 109.32 0 493.1081 482 1 383.788 1 113.745 0 0 658 37 0 0 0 658 37 2 0 0 1 52.55547 51.0152 50 166.135 0 139.2432 141 0 -26.8921 0 53.6138 28.5013 0 0 .0297486 7.790303 87.61113 7.870513 16.74383 7.7903 7.87051 43.0493 12.7587 27.9386 52.5555 6773.81 2647.39 -53.5120150807535 -.574784386460464 -1.82937456860159 -.3266540915 -1.085
5 .0336142 2647 6798 6798 2647 1 .1914723524 1 1 0 0 0 0 0 0 0 0 0 0 315.9162 85.71438 1 31.88617 44.69122 43 108.515 0 1533.306 1515 1 1424.79 1 315.916 0 0 638 36 1 0 0 638 36 0 0 0 1 70.96976 51.03292 51 165.175 0 199.1667 201.5 0 33.992 1 85.7144 0 0 0 .642645 8.584438 286.7416 7.858472 25.45528 8.58444 7.85847 143.807 31.8862 28.1447 70.9698 6798.44 2647.3 -90.2239347457086 -2.5101918695503 -2.62742120660848 -.566518157 -1.882
6 .0815126 2646 6824 6824 2646 1 .07725851793 1 1 0 0 0 0 0 0 0 0 0 0 1007.216 534.1279 1 100.8223 42.6837 42 107.773 0 4468.027 4353 1 4360.25 1 1007.22 0 0 724 37 0 0 0 724 37 0 0 0 1 86.24736 50.14779 50 164.173 0 384.5405 382 1 220.368 1 534.128 0 0 0 .799393 5.951692 765.9261 7.668728 54.22463 5.95169 7.66873 436.461 100.822 35.5835 86.2474 6824.45 2646.74 -121.776042234037 -3.44015651484457 -29.6095241460622 -.2754772954 -.915
7 .0543869 2646 6849 6849 2646 1 .09015734301 1 1 0 0 0 0 0 0 0 0 0 0 866.968 325.9866 1 86.81377 42.92768 42 107.073 0 3860.056 3719.5 1 3752.98 1 866.968 0 0 719 36 1 0 0 719 36 1 0 0 1 75.13765 50.29346 50 163.189 0 297.7222 299.5 0 134.533 1 325.987 0 0 0 .516116 6.193068 562.1751 7.233191 34.11628 6.19307 7.23319 375.805 86.8138 31.009 75.1377 6849.75 2646.64 -117.5431877536 -5.60987917993055 -18.3686089989426 -.4248033018 -1.411
8 .0809838 2647 6875 6875 2647 1 .08144140912 1 1 0 0 0 0 0 0 0 0 0 0 965.7532 445.213 1 96.68046 43.8091 43 106.434 0 4284.769 4038 1 4178.34 1 965.753 0 0 681 39 0 0 0 681 39 1 0 0 1 80.89397 49.86637 50 162.218 0 346.3846 342 1 184.166 1 445.213 0 0 0 .559016 6.912817 795.6348 7.461947 40.16323 6.91282 7.46195 418.288 96.6805 33.4625 80.894 6875.21 2647.04 -120.573228565207 -4.43910881670381 -25.269394545625 -.3362983521 -1.117
10 .032244 2646 6926 6926 2646 1 .2822417208 1 1 0 0 0 0 0 0 0 0 0 0 128.4748 56.14929 1 13.97194 43.01762 42 105.208 0 561.4474 572.5 1 456.239 1 128.475 0 0 738 38 0 0 0 738 38 2 0 0 1 55.04087 49.99593 50 160.326 0 156.4211 155 0 -3.90473 0 56.1493 28.5013 0 0 .442928 5.863066 88.68886 7.759005 25.88084 5.86307 7.759 49.6171 13.9719 27.9386 55.0409 6926.13 2646.78 -58.2947522598211 -.692948971520288 -.144187779317578 -.3594734982 -1.194
11 .0172422 2646 6951 6951 2646 1 .6239281612 1 1 0 0 0 0 0 0 0 0 0 0 14.39047 21.75746 1 14.16329 43.12797 43 104.559 0 123.0857 120 0 18.5271 0 14.3905 24.1017 0 758 35 2 0 0 758 35 2 0 0 1 21.32795 50.28628 50 159.431 0 151.7714 148 0 -7.65935 0 21.7575 28.5013 0 0 .395549 5.759443 19.30768 7.43913 23.13653 5.75944 7.43913 19.5895 14.1633 27.9386 21.328 6951.28 2646.35 -1.79202651455113 0 -.3201271341467 0 0
12 .0466213 2646 6976 6976 2646 1 .09678745539 1 1 0 0 0 0 0 0 0 0 0 0 1013.848 268.0198 1 101.4806 42.50275 42 103.986 0 4587.324 4369 1 4483.34 1 1013.85 0 0 726 37 0 0 0 726 37 0 0 0 1 72.8686 50.66804 50 158.627 0 269.1351 262 0 110.508 1 268.02 0 0 0 .804145 5.528047 936.7101 7.595189 41.72473 5.52805 7.59519 448.758 101.481 30.0448 72.8686 6976.82 2646.51 -122.56172827962 -8.62436582049934 -14.6156680949951 -.5778057864 -1.919
13 .0376262 2646 7002 7002 2646 1 .2971025304 1 1 0 0 0 0 0 0 0 0 0 0 109.7394 52.85042 1 12.3784 43.10302 43 103.501 0 477.1944 477.5 1 373.694 1 109.739 0 0 728 36 2 0 0 728 36 0 0 0 1 51.80712 51.72527 51 157.687 0 132.2778 128.5 0 -25.409 0 52.8504 28.5013 0 0 .643194 5.555927 122.8362 8.373589 22.54723 5.55593 8.37359 42.1519 12.3784 27.9386 51.8071 7002.32 2646.6 -52.7780539793136 -.544383102597763 -1.67778690951728 -.3173143445 -1.054
14 .01146 2646 7027 7027 2646 1 .5673964353 1 1 0 0 0 0 0 0 0 0 0 0 17.23766 23.6819 1 12.79667 43.45804 43 103.068 0 129.5789 127.5 0 26.5112 1 17.2377 0 0 703 38 1 0 0 703 38 0 0 0 1 23.21441 50.87055 51 156.872 0 148.6053 150 0 -8.26636 0 23.6819 28.5013 0 0 .55192 6.121806 23.70384 7.689044 27.86797 6.12181 7.68904 19.681 12.7967 27.9386 23.2144 7027.91 2646.48 -3.12016467126315 0 -.352153638488553 0 0
15 .0360019 2646 7052 7052 2646 1 .2874688449 1 1 0 0 0 0 0 0 0 0 0 0 121.2988 54.91808 1 13.28641 43.79913 43 102.801 0 539.1081 532 1 436.308 1 121.299 0 0 687 37 0 1 0 687 37 2 0 0 1 53.83397 50.47307 50 156.138 0 140.5405 142 0 -15.597 0 54.9181 28.5013 0 0 .474066 6.723645 139.4019 7.198078 29.08378 6.72365 7.19808 47.7908 13.2864 27.9386 53.834 7052.93 2646.73 -57.0561875465684 -.635916025053366 -.819917154822464 -.3441410456 -1.143
16 .110273 2646 7078 7078 2646 1 .07846735886 1 1 0 0 0 0 0 0 0 0 0 0 1478.434 577.3517 1 147.9027 44.4841 43 102.711 0 6988.486 6822 1 6885.77 1 1478.43 0 0 692 35 0 0 0 692 35 3 0 0 1 90.02117 51.2341 51 155.344 0 388.8857 362 1 233.542 1 577.352 0 0 0 .54659 8.321578 1402.245 7.611789 111.2464 8.32158 7.61179 688.854 147.903 36.4141 90.0212 7078.46 2646.84 -134.673107288205 -6.71038907980183 -31.0622414571738 -.4083616419 -1.357
17 .0568094 2646 7103 7103 2646 1 .179054807 1 1 0 0 0 0 0 0 0 0 0 0 313.4862 105.2254 1 31.60544 42.0566 41 102.459 0 1622.865 1598 1 1520.41 1 313.486 0 0 689 37 1 0 0 689 37 0 0 0 1 72.02556 51.08999 50 154.741 0 196 195 0 41.2595 1 105.225 0 0 0 .601268 5.808323 336.9903 7.975109 34.42464 5.80832 7.97511 153.286 31.6054 28.2417 72.0256 7103.42 2646.7 -92.0544590384857 -2.09139720125664 -3.55475396491938 -.4740979287 -1.575
18 .0398839 2646 7129 7129 2646 1 .4520471663 1 1 0 0 0 0 0 0 0 0 0 0 30.02804 30.47036 1 9.958165 41.90515 41.5 102.269 0 163.9459 166 0 61.6766 1 30.028 0 0 738 37 0 0 0 738 37 0 0 0 1 29.86886 50.45393 50 154.073 0 134.7838 136 0 -19.2894 0 30.4704 28.5013 0 0 .00202103 5.258238 28.91938 7.218901 19.75564 5.25824 7.2189 20.4537 9.95816 27.9386 29.8689 7129.46 2646.66 -10.9305243078239 0 -1.11228426323749 0 0
19 .0665009 2646 7154 7154 2646 1 .1433550231 1 1 0 0 0 0 0 0 0 0 0 0 370.4043 157.7385 1 37.24738 42.5097 42 102.061 0 1944.324 1892 1 1842.26 1 370.404 0 0 722 37 0 0 0 722 37 0 0 0 1 73.31307 50.76039 51 153.365 0 214.9189 211 0 61.5537 1 157.739 0 0 0 .716839 5.611366 271.5703 7.553191 38.03316 5.61137 7.55319 185.256 37.2474 28.6087 73.3131 7154.73 2646.46 -97.4679313539752 -2.0129888562948 -6.56602546407224 -.3707381967 -1.232
20 .0513896 2646 7179 7179 2646 1 .243475704 1 1 0 0 0 0 0 0 0 0 0 0 67.56324 194.6987 1 8.031907 42.3347 42 101.709 0 405.0769 413 1 303.368 1 67.5632 0 0 732 39 0 0 0 732 39 0 0 0 1 66.86233 51.20765 51 153.19 0 238.2308 240 0 85.0408 1 194.699 0 0 0 .654449 6.290613 69.87334 7.304444 45.69721 6.29061 7.30444 36.0643 8.03191 29.2042 66.8623 7179.9 2646.52 -47.0749216238704 -1.22883695014691 -10.4231716376403 .4596525096 1.527
21 -.0081613 2646 7205 7205 2646 1 .2370805615 1 1 0 0 0 0 0 0 0 0 0 0 214.016 66.22998 1 21.8162 43.00593 42 101.797 0 1087.789 1089 1 985.992 1 214.016 0 0 674 38 0 0 0 674 38 0 0 0 1 65.23095 50.87537 51 152.921 0 180.1842 171 0 27.2636 0 66.23 28.5013 0 0 .508886 6.721589 209.135 7.733251 37.06813 6.72159 7.73325 100.509 21.8162 28.0713 65.2309 7205.7 2646.59 -79.8590773439986 -1.49940690173901 -1.86819534092053 -.5093916749 -1.692

Total number of rows: 13048

Table truncated, full table size 5571 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table
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