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Sample GSM280322 Query DataSets for GSM280322
Status Public on Aug 20, 2008
Title C1 evolved M2 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 M2
Organism(s) Saccharomyces cerevisiae
Characteristics M2
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/2008-02/78817.gif
Genotype: M2
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 .00866884 2649 348 348 2649 1 .06164519634 1 1 0 0 0 0 0 0 0 0 0 0 1800.862 1823.391 1 180.4373 41.78731 41 95.2546 0 1404.314 1403 1 1309.06 1 1800.86 0 0 851 35 0 1 0 851 35 2 0 0 1 183.3096 50.17861 49 110.301 0 762.8 751 1 652.499 1 1823.39 0 0 0 .644214 5.359818 146.9365 7.958928 62.2305 5.35982 7.95893 131.161 180.437 65.5972 183.31 348.109 2649.5 -119.797789676769 -.0314212154236044 -103.251957796334 .005399293663 .018
2 .0314183 2650 373 373 2650 1 .6031446289 1 1 0 0 0 0 0 0 0 0 0 0 14.70871 15.29894 1 14.44276 41.83924 42 94.8668 0 83 83 0 -11.8668 0 14.7087 11.622 0 734 38 2 0 0 734 38 1 0 0 1 15.0161 49.59537 49 109.93 0 95.86842 96 0 -14.0613 0 15.2989 8.64685 0 0 .104273 5.172209 13.98455 7.406795 18.42321 5.17221 7.40679 8.17854 14.4428 6.74102 15.0161 373.5 2650 -3.47516526079281 0 -6.09022367032965 0 0
3 .0194468 2649 399 399 2649 1 .6033410514 1 1 0 0 0 0 0 0 0 0 0 0 14.75794 15.60695 1 14.4911 42.3036 42 94.4844 0 79 79 0 -15.4844 0 14.7579 11.6765 0 751 35 2 1 0 751 35 0 0 0 1 15.31842 49.6751 49 109.492 0 92.6 90 0 -16.8921 0 15.607 8.80911 0 0 .0258659 5.321251 9.22911 7.499931 11.33501 5.32125 7.49993 8.17854 14.4911 6.74102 15.3184 399.262 2649.39 -5.26170234737615 0 -8.00263939441045 0 0
4 .262999 2649 424 424 2649 1 .0634067526 1 1 0 0 0 0 0 0 0 0 0 0 751.5576 638.5572 1 75.99613 43.36123 42 94.1118 0 639.4857 624 1 545.374 1 751.558 0 0 681 35 2 0 0 681 35 1 0 0 1 66.91021 51.13363 50 108.876 0 324.2571 321 1 215.382 1 638.557 0 0 0 .55598 6.976551 78.07703 8.761953 68.88923 6.97655 8.76195 55.1472 75.9961 22.5684 66.9102 424.593 2649.8 -93.2080386152392 -.577708150786352 -70.1682197802062 -.07076247405 -.235
5 .354593 2650 449 449 2650 1 .06157629473 1 1 0 0 0 0 0 0 0 0 0 1 2289.508 2265.08 1 229.235 43.85385 42 93.7489 0 1734.676 1684 1 1640.93 1 2289.51 0 0 650 37 2 0 0 650 37 0 0 0 1 227.3857 51.14769 50 108.286 0 873.2703 858 1 764.984 1 2265.08 0 0 0 .699138 7.809472 296.431 9.038509 184.106 7.80947 9.03851 164.296 229.235 76.7949 227.386 449.654 2650.09 -126.664670500954 -.0270147201262287 -108.013597348968 -.004658718527 -.015
6 .104767 2649 474 474 2649 1 .06168512282 1 1 0 0 0 0 0 0 0 0 0 1 5301.886 4631.403 1 530.3133 42.88935 43 93.3585 0 3864.684 3832.5 1 3771.33 1 5301.89 0 0 723 38 1 0 0 723 38 0 0 0 1 463.5722 49.83264 50 107.799 0 1668.316 1609.5 1 1560.52 1 4631.4 0 0 0 .841771 5.95146 670.8217 7.431753 315.1628 5.95146 7.43175 377.221 530.313 156.197 463.572 474.827 2649.77 -151.959884437333 -.467055281013895 -129.368199201013 -.05871785218 -.195
7 .0475641 2649 500 500 2649 1 .06147077046 1 1 0 0 0 0 0 0 0 0 0 1 6441.666 6779.628 1 644.2697 43.4375 43 92.9717 0 4663.625 4530.5 1 4570.65 1 6441.67 0 0 688 32 3 0 0 688 32 6 0 0 1 678.2596 50.45785 50 107.376 0 2385.281 2265 1 2277.9 1 6779.63 0 0 0 .617344 5.885777 801.5073 7.898996 543.3472 5.88578 7.899 457.138 644.27 227.89 678.26 500.382 2649.76 -157.803547458297 -.143938785531697 -140.701144741211 .02220772176 .074
8 .174451 2651 524 524 2651 1 .06360806893 1 1 0 0 0 0 0 0 1 0 0 0 7302.781 11070.66 1 730.3691 44.65396 44 92.5377 0 5272.364 5111 1 5179.83 1 7302.78 0 0 656 33 0 0 0 656 33 4 0 0 1 1107.247 51.69817 51 106.961 0 3840.091 3207 1 3733.13 1 11070.7 0 0 0 .526351 7.359726 1225.818 8.910602 1584.021 7.35973 8.9106 518.047 730.369 373.374 1107.25 524.469 2651.19 -161.607018299194 -2.34651669154686 -155.503405192008 .1806853888 .6
10 .103738 2649 577 577 2649 1 .06367087626 1 1 0 0 0 0 0 0 0 0 0 1 631.3124 600.003 1 64.09434 42.40499 42 91.6358 0 558.0769 583 1 466.441 1 631.312 0 0 721 39 0 0 0 721 39 0 0 0 1 63.52393 50.71151 50 106.157 0 300.0256 305 1 193.869 1 600.003 0 0 0 .712035 5.768177 104.7549 7.792446 44.74047 5.76818 7.79245 47.3557 64.0943 20.5254 63.5239 577 2649.43 -88.4679938630397 -.13749572389069 -67.0490668450188 -.02209091006 -.073
11 .126624 2649 601 601 2649 1 .1111673348 1 1 0 0 0 0 0 0 0 0 0 1 91.65734 129.9383 1 14.61463 42.82167 43 91.1465 0 157 156 1 65.8535 1 91.6573 0 0 729 27 3 0 0 729 27 7 3 0 1 23.97325 50.93553 50 105.819 0 149.2963 149 1 43.4776 1 129.938 0 0 0 .0352343 5.745139 19.66058 8.398061 16.54554 5.74514 8.39806 10.5003 14.6146 8.02149 23.9732 601.357 2649.73 -31.126182598398 -.762595918279182 -25.3118142973379 .1515697993 .504
12 .12115 2649 627 627 2649 1 .06176556125 1 1 0 0 0 0 0 0 0 0 0 1 9193.691 10820.69 1 919.4385 43.18388 43 90.6426 0 6744.167 6570.5 1 6653.52 1 9193.69 0 0 707 36 0 0 0 707 36 0 0 0 1 1082.257 50.529 50 105.377 0 3728 3580 1 3622.62 1 10820.7 0 0 0 .830961 6.10207 1103.566 7.706566 835.422 6.10207 7.70657 665.403 919.439 362.325 1082.26 627.256 2649.5 -169.218426277388 -.598743483083396 -154.602992118295 .07076523166 .235
13 .10057 2649 652 652 2649 1 .0636008228 1 1 0 0 0 0 0 0 0 0 0 0 786.8097 640.0227 1 79.41889 43.08796 43 90.2335 0 686 687.5 1 595.766 1 786.81 0 0 739 38 0 0 0 739 38 1 0 0 1 67.31285 51.48173 51 104.971 0 311.8947 318 1 206.924 1 640.023 0 0 0 .555404 5.966401 83.56645 7.952646 41.15678 5.9664 7.95265 60.1354 79.4189 21.7627 67.3129 652.949 2649.4 -95.8891141278033 -.799826533260116 -68.9799745136742 -.08967437079 -.298
14 .10777 2649 678 678 2649 1 .1504228401 1 1 0 0 0 0 0 0 0 0 0 1 76.87317 65.45518 1 13.88854 43.3052 43 89.8044 0 144.1579 145 1 54.3535 1 76.8732 0 0 711 38 0 0 0 711 38 1 0 0 1 20.29901 51.01266 50 104.589 0 127.5526 127 0 22.9633 1 65.4552 0 0 0 .171715 6.337766 21.14241 7.910671 18.23673 6.33777 7.91067 9.81995 13.8885 7.12141 20.299 678.86 2649.53 -26.2277186434564 -.192138313919422 -12.2647125627841 -.06983077469 -.232
15 .173009 2649 703 703 2649 1 .06381195101 1 1 0 0 0 0 0 0 0 0 0 1 639.8126 570.0737 1 64.8546 43.0452 42 89.3692 0 582.6786 573.5 1 493.309 1 639.813 0 0 708 28 3 1 0 708 28 0 0 0 1 60.63875 51.17938 51 104.256 0 290.1786 286.5 1 185.923 1 570.074 0 0 0 .357805 6.225666 45.51439 7.798036 53.81729 6.22567 7.79804 50.0043 64.8546 19.7766 60.6387 703.488 2649.5 -90.1655258871042 -.36433162861061 -65.8106893928155 -.05012175964 -.167
16 .214307 2649 729 729 2649 1 .0617793657 1 1 0 0 0 0 0 0 0 0 0 1 14316.11 12112.92 1 1431.654 43.70537 43 88.9367 0 10738.68 10653.5 1 10649.7 1 14316.1 0 0 689 34 1 0 0 689 34 0 3 0 1 1211.451 51.24964 50 103.909 0 4263.529 4348.5 1 4159.62 1 12112.9 0 0 0 .841975 7.113408 933.1915 8.821968 401.6338 7.11341 8.82197 1065.01 1431.65 416.017 1211.45 729.109 2649.5 -183.518391138762 -.619630938294892 -158.744973664858 -.07257647273 -.241
17 .0820605 2649 754 754 2649 1 .06152766603 1 1 0 0 0 0 0 0 0 0 0 1 2764.794 2835.279 1 276.6803 42.48291 42 88.4891 0 2233.378 2122 1 2144.89 1 2764.79 0 0 702 37 0 0 0 702 37 0 0 0 1 284.2417 50.62821 50 103.502 0 1052.946 1032 1 949.444 1 2835.28 0 0 0 .841978 5.896068 415.9579 7.875272 197.2156 5.89607 7.87527 214.645 276.68 95.1834 284.242 754.195 2649.52 -134.805169418198 -.0660250913297334 -114.482859547438 .01093305042 .036
18 -.00188414 2649 779 779 2649 1 .1209500638 1 1 0 0 0 0 0 0 0 0 0 1 85.58628 99.43374 1 13.77848 42.55447 42 88.09 0 152.9143 152 1 64.8242 1 85.5863 0 0 716 35 2 0 0 716 35 1 0 0 1 21.71287 50.20531 50 103.103 0 137.8286 139 1 34.7257 1 99.4337 0 0 0 .134762 5.536513 15.5835 7.710208 24.26385 5.53651 7.71021 10.436 13.7785 7.58288 21.7129 779.732 2649.48 -30.7131956053093 -.22896898529153 -20.1425155270944 .06512962503 .216
19 .00383753 2649 805 805 2649 1 .06153249511 1 1 0 0 0 0 0 0 0 0 0 1 2592.302 2607.693 1 259.4348 42.76138 42 87.7584 0 2145.973 2049 1 2058.21 1 2592.3 0 0 725 37 0 0 0 725 37 0 0 0 1 261.5241 50.9131 51 102.729 0 988.1081 902 1 885.379 1 2607.69 0 0 0 .746565 5.79194 296.4055 7.765692 198.9577 5.79194 7.76569 205.984 259.435 88.7942 261.524 805.2 2649.43 -133.551366326173 -.0147206039634296 -112.390533657168 .002570943989 .009
20 .110926 2649 830 830 2649 1 .06731953616 1 1 0 0 0 0 0 0 0 0 0 0 336.4826 467.6814 1 35.13223 42.56911 42 87.4974 0 359.8889 362.5 1 272.391 1 336.483 0 0 738 36 0 0 0 738 36 1 0 0 1 50.80529 50.3252 50 102.322 0 261.1667 247 1 158.844 1 467.681 0 0 0 .422439 5.697839 41.52849 8.0492 51.37454 5.69784 8.0492 28.4405 35.1322 17.2556 50.8053 830.563 2649.4 -72.2073926177816 -1.47276724734078 -61.1660341765566 .1429874548 .475
21 .171481 2649 856 856 2649 1 .06184274912 1 1 0 0 0 0 0 0 0 0 0 1 1584.584 1771.699 1 158.7718 42.5288 42 87.1935 0 1386.923 1351 1 1299.73 1 1584.58 0 0 677 39 1 0 0 677 39 0 0 0 1 178.2613 50.97341 50 101.855 0 708.2308 686 1 606.375 1 1771.7 0 0 0 .673948 6.533787 189.615 9.225601 147.1883 6.53379 9.2256 130.23 158.772 61.0111 178.261 856 2649.5 -119.580424218938 -.363376038737445 -101.057663000453 .04847464336 .161

Total number of rows: 13048

Table truncated, full table size 5548 Kbytes.




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

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