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Sample GSM280305 Query DataSets for GSM280305
Status Public on Aug 20, 2008
Title C1 evolved M5 vs YFP 2
Sample type RNA
 
Channel 1
Source Name YFP
Organism(s) Saccharomyces cerevisiae
Characteristics YFP
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 M5
Organism(s) Saccharomyces cerevisiae
Characteristics M5
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/2008-02/78820.gif
Genotype: M5
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 .123223 2645 9872 9872 2645 1 .06609892806 1 1 0 0 0 0 0 0 0 0 0 0 12901.87 7132.706 1 1297.901 44.77535 44 235.439 0 7880.351 7618 1 7644.91 1 12901.9 0 0 779 37 0 0 0 779 37 1 0 0 1 714.3488 64.61489 63 485.032 0 30852.3 31167 1 30367.3 1 7132.71 0 0 0 .79973 6.428536 1396.906 11.95162 3877.45 6.42854 11.9516 769.062 1297.9 3041.32 714.349 9872.59 2645.21 -99.0147168173296 -4.00635415334712 -126.738544418612 -.2573985076 -.855
2 .118749 2645 9897 9897 2645 1 .7618373709 1 1 0 0 0 0 0 0 0 0 0 0 132.9142 40.3831 1 130.3467 46.94618 46 237.813 0 122.3429 120 0 -115.47 0 132.914 142.743 0 706 35 0 0 0 706 35 3 0 0 1 39.68294 68.30595 67.5 487.486 0 241.6 238 0 -245.886 0 40.3831 169.981 0 0 .118216 7.039499 19.69464 11.65156 38.66614 7.0395 11.6516 83.7233 130.347 167.034 39.6829 9897.6 2645.15 -3.19868892190671 0 -3.56298392048594 0 0
3 .183744 2645 9924 9924 2645 1 .7414899858 1 1 0 0 0 0 0 0 0 0 0 0 122.9648 40.71827 1 120.5894 47.88372 47 240.328 0 126.9737 121.5 0 -113.354 0 122.965 133.154 0 731 38 0 0 0 731 38 0 0 0 1 40.0123 69.62927 69 490.471 0 274.6579 280 0 -215.814 0 40.7183 169.981 0 0 .658585 6.860161 25.26239 11.63418 68.57321 6.86016 11.6342 83.7233 120.589 167.034 40.0123 9924.29 2645.6 -3.10751470805961 0 -2.90228815145743 0 0
4 .223715 2645 9948 9948 2645 1 .2551978351 1 1 0 0 0 0 0 0 0 0 0 0 289.6522 213.7243 1 141.3801 47.42401 47 243.044 0 418.2895 427.5 0 175.245 1 289.652 0 0 658 38 0 1 0 658 38 0 0 0 1 39.39904 71.41793 68 493.973 0 1572.553 1620.5 1 1078.58 1 213.724 0 0 0 .879477 7.063174 74.02443 16.86693 304.6761 7.06317 16.8669 85.5377 141.38 198.831 39.399 9948.44 2645.03 -6.0950611452424 -.218300914493256 -25.8744862040959 -.1320230411 -.439
5 .343045 2645 9973 9973 2645 1 .07103398495 1 1 0 0 0 0 0 0 0 0 0 1 1735.271 1428.051 1 211.7372 46.14218 46 245.739 0 1443.154 1409 1 1197.42 1 1735.27 0 0 633 39 0 0 0 633 39 0 0 0 1 147.2122 71.18957 64 497.975 0 7170.026 6778 1 6672.05 1 1428.05 0 0 0 .875072 7.584044 272.2763 26.5707 1415.747 7.58404 26.5707 146.108 211.737 687.796 147.212 9973.11 2645.8 -45.7325583886307 -.631653018851513 -79.4496493276984 -.0846234268 -.281
6 .190379 2645 9999 9999 2645 1 .06267136128 1 1 0 0 0 0 0 0 0 0 0 1 4247.572 4736.821 1 440.1523 44.98507 45 248.612 0 3330.45 3306 1 3081.84 1 4247.57 0 0 670 40 0 0 0 670 40 0 0 0 1 475.0421 64.58209 62 502.465 0 22529.58 21976 1 22027.1 1 4736.82 0 0 0 .977583 6.045153 654.8491 13.49445 4224.737 6.04515 13.4944 319.354 440.152 2209.04 475.042 9999.19 2645.27 -72.6664801812082 -.34681854769072 -116.702749564718 .04734625121 .157
7 .359946 2645 10024 10024 2645 1 .06252546332 1 1 0 0 0 0 0 0 0 0 0 1 4371.236 4292.91 1 450.9865 45.72303 45 251.58 0 3549.875 3540 1 3298.3 1 4371.24 0 0 686 40 0 0 0 686 40 0 0 0 1 430.7881 76.1895 71 507.605 0 20490.3 19352 1 19982.7 1 4292.91 0 0 0 .942656 7.122021 570.6936 23.16483 3690.106 7.12202 23.1648 340.29 450.987 2005.24 430.788 10024.5 2645 -74.6283965302702 -.0457296943836452 -113.658929683606 -.00785248404 -.026
8 .425395 2645 10049 10049 2645 1 .06265131815 1 1 0 0 0 0 0 0 0 0 0 1 3924.293 4033.597 1 406.7598 47.44709 46 254.454 0 3324.55 3354 1 3070.1 1 3924.29 0 0 671 40 0 0 0 671 40 0 0 0 1 404.9493 87.4158 80 513.348 0 19309.17 18464 1 18795.8 1 4033.6 0 0 0 .946621 8.41373 665.3855 30.42753 3607.997 8.41373 30.4275 318.221 406.76 1886.99 404.949 10049.7 2645.16 -72.5561989773023 -.0711086124742716 -111.745756543359 .0119310152 .04
10 .794794 2644 10100 10100 2644 1 .1560354444 1 1 1 0 0 0 1 0 0 0 0 1 363.3001 317.305 1 112.9323 65.82329 60 264.005 0 548.4615 550 0 284.456 1 363.3 0 0 730 39 0 0 0 730 39 0 0 0 1 46.36396 153.3699 129.5 526.095 0 2093.923 2072 1 1567.83 1 317.305 0 0 0 .768108 22.57711 74.724 84.59255 283.1724 22.5771 84.5925 88.4237 112.932 229.088 46.364 10100.8 2644.79 -12.1191372666502 -.150981000373868 -35.8220827575699 -.05878865184 -.195
11 .758244 2644 10125 10125 2644 1 .6643064482 1 1 0 0 0 0 1 0 0 0 0 0 86.65279 42.29212 1 84.97888 74.34225 70 268.94 0 202.6757 198 0 -66.2648 0 86.6528 97.4598 0 748 37 1 0 0 748 37 2 0 0 1 41.55886 182.5481 160.5 533.832 0 464.8919 467 0 -68.9401 0 42.2921 169.981 0 0 .525598 22.13094 27.38213 82.27929 51.7219 22.1309 82.2793 83.7233 84.9789 167.034 41.5589 10125.9 2644.58 -1.36151074304536 0 -.542405710503864 0 0
12 .726736 2644 10151 10151 2644 1 .06351340805 1 1 0 0 0 0 1 0 0 0 0 1 3417.972 4583.25 1 355.1181 74.58784 70 272.691 0 3242.697 3176 1 2970.01 1 3417.97 0 0 740 33 6 0 0 740 33 6 0 0 1 459.7247 188.5568 170 542.343 0 21899.48 21680 1 21357.1 1 4583.25 0 0 0 .724583 22.10907 590.102 78.09829 2992.018 22.1091 78.0983 308.576 355.118 2142.24 459.725 10151.7 2644.88 -71.5989511733216 -1.3481325590071 -115.737515686826 .127405155 .423
13 .74255 2644 10176 10176 2644 1 .1136737 1 1 0 0 0 0 1 0 0 0 0 1 464.3214 482.5822 1 108.7838 80.6568 74 275.481 0 670.641 688 0 395.16 1 464.321 0 0 743 39 0 0 0 743 39 1 0 0 1 59.32246 211.0363 197 550.824 0 2887.231 2809 1 2336.41 1 482.582 0 0 0 .789939 24.85883 83.10567 84.13365 402.5427 24.8588 84.1337 92.5802 108.784 287.208 59.3225 10176.7 2644.9 -18.0730374286126 -.0541197380625403 -47.3534208267999 .01675260027 .056
14 .684617 2645 10202 10202 2645 1 .6535004999 1 1 0 0 0 0 1 0 0 0 0 0 81.47035 42.58044 1 79.89655 80.66805 76 281.292 0 191.6216 192 0 -89.6707 0 81.4704 92.2557 0 723 37 1 0 0 723 37 2 0 0 1 41.84219 230.065 214 556.735 0 492.0811 488 0 -64.654 0 42.5804 169.981 0 0 .0222902 22.93017 21.18746 93.82922 55.53146 22.9302 93.8292 83.7233 79.8966 167.034 41.8422 10202.4 2645 -2.15747063798427 0 -.498116771401651 0 0
15 .779036 2644 10227 10227 2644 1 .1462886075 1 1 1 0 0 0 1 0 0 0 0 1 322.8139 355.2409 1 103.0393 88.46341 82 284.229 0 560.4324 551 0 276.203 1 322.814 0 0 738 37 0 0 0 738 37 0 0 0 1 49.03408 264.7317 243.5 566.032 0 2321.622 2236 1 1755.59 1 355.241 0 0 0 .726684 29.36583 74.54735 112.5125 209.2322 29.3658 112.513 88.1616 103.039 242.325 49.0341 10227.6 2644.67 -11.6587732741959 -.109981201738086 -39.0185102950196 .04157071675 .138
16 .677391 2644 10253 10253 2644 1 .06386523739 1 1 0 0 0 0 0 0 0 0 0 1 4143.794 6105.125 1 424.1875 93.86115 90 286.716 0 4112.179 4021 1 3825.46 1 4143.79 0 0 713 39 0 0 0 713 39 0 0 0 1 611.5787 284.7475 275 579.043 0 28829.15 27877 1 28250.1 1 6105.12 0 0 0 .926735 27.28288 488.9418 99.9623 3317.819 27.2829 99.9623 391.601 424.187 2829.94 611.579 10253.1 2644.88 -78.9194636998674 -2.07524072036924 -124.479558392129 .1682963392 .559
17 .679061 2644 10278 10278 2644 1 .06806461426 1 1 0 0 0 0 0 0 0 0 0 1 1441.473 1456.058 1 170.5287 84.46512 82 289.926 0 1614.486 1609 1 1324.56 1 1441.47 0 0 731 35 2 0 0 731 35 1 0 0 1 149.9133 236.6785 225 596.832 0 7413.543 7246 1 6816.71 1 1456.06 0 0 0 .922864 22.34217 201.7738 78.83031 953.6114 22.3422 78.8303 156.698 170.529 701.837 149.913 10278.4 2644.79 -48.5473335907462 -.0228331715615862 -80.1160746621236 .004372152151 .015
18 .648299 2644 10303 10303 2644 1 .648081224 1 1 0 0 0 0 0 0 0 0 0 0 78.54496 42.75294 1 77.02768 82.79728 80 295.234 0 260.1622 260 0 -35.0718 0 78.545 89.3034 0 735 37 0 2 0 735 37 0 0 0 1 42.16568 225.7687 216 607.991 0 751.1351 751 0 143.144 0 42.7529 169.981 0 0 .304984 21.3034 27.29012 75.45725 70.48095 21.3034 75.4572 83.7233 77.0277 167.646 42.1657 10303.9 2644.52 -.552854377248816 0 -1.5376679000562 0 0
19 .658841 2644 10329 10329 2644 1 .06494538557 1 1 0 0 0 0 0 0 0 0 0 1 2028.938 1958.039 1 221.8633 90.34663 88 299.925 0 2192.341 2118 1 1892.42 1 2028.94 0 0 727 41 0 0 0 727 41 0 0 0 1 199.0678 247.9546 236 620.367 0 9730.61 9166 1 9110.24 1 1958.04 0 0 0 .934461 23.63912 294.4405 83.57852 1613.331 23.6391 83.5785 206.935 221.863 926.21 199.068 10329 2644.73 -58.6473332722978 -.0904471911285292 -89.1416463035424 -.0154475495 -.051
20 .626845 2644 10354 10354 2644 1 .6466957482 1 1 0 0 0 0 0 0 0 0 0 0 78.10436 42.77957 1 76.59559 86.63984 85 302.98 0 293.25 290 0 -9.73017 0 78.1044 88.8578 0 733 32 5 0 0 733 32 6 0 0 1 42.05104 235.382 231 641.798 0 683.625 673.5 0 41.8267 0 42.7796 169.981 0 0 .445879 22.15978 39.63788 72.31544 88.07502 22.1598 72.3154 83.7233 76.5956 167.087 42.051 10354.8 2644.26 -.117213143175205 0 -.286442259864007 0 0
21 .65525 2644 10380 10380 2644 1 .08394293461 1 1 0 0 0 0 0 0 0 0 0 0 682.5781 823.7695 1 114.2477 81.48811 80 306.67 0 930.4474 904.5 1 623.777 1 682.578 0 0 715 38 0 0 0 715 38 0 0 0 1 89.53274 221.2993 206 652.402 0 4575.526 4386 1 3923.12 1 823.77 0 0 0 .868842 23.7966 128.5295 84.59793 693.3727 23.7966 84.5979 104.406 114.248 426.391 89.5327 10380.2 2644.72 -28.4343079888143 -.480578963607352 -63.0368291199972 .08165339542 .271

Total number of rows: 13048

Table truncated, full table size 5552 Kbytes.




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

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