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Sample GSM65088 Query DataSets for GSM65088
Status Public on Jul 22, 2005
Title trr - 0.3 mM H2O2 - 10 min
Sample type RNA
 
Channel 1
Source name time = 0 min
Organism Saccharomyces cerevisiae
Characteristics time = 0 min
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name time =10 min
Organism Saccharomyces cerevisiae
Characteristics time =10 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6685.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jul 21, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2658
Series (1)
GSE2977 Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1D_MEAN The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEAN Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PIX_RAT2_MEDIAN Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale
TOT_SPIX Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale
TOT_BPIX Number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG User defined spot flag (default 0).; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1B_MEAN CH2B_MEAN PERGTBCH1I_1SD PERGTBCH2I_1SD PIX_RAT2_MEDIAN TOT_SPIX TOT_BPIX REGR CORR TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN RAT1N_MEAN VALUE
1 1644 2913 455 818 1189 2095 462 847 55 59 1.705 225 990 1.799 .938 31 48 66 83 0 2942 826 2116 1.78 .562 .832
2 642 1231 449 789 193 442 456 825 12 18 2.205 225 705 1.777 .857 31 48 83 100 0 1243 796 447 2.316 .432 1.212
3 1403 2388 461 800 942 1588 468 838 49 50 1.546 225 720 1.691 .945 31 48 100 117 0 2412 808 1604 1.703 .587 .768
4 734 1271 462 823 272 448 471 866 13 14 1.679 225 720 1.699 .915 31 48 118 135 0 1283 831 452 1.662 .602 .733
5 764 1350 471 860 293 490 477 900 20 20 1.729 225 720 1.515 .92 31 48 135 152 0 1363 868 495 1.689 .592 .757
6 615 1171 478 905 137 266 486 922 9 13 2.173 225 720 1.767 .896 31 48 153 170 0 1182 914 268 1.956 .511 .968
7 1034 1878 485 923 549 955 503 955 35 37 1.756 225 720 1.609 .934 31 48 170 187 0 1896 932 964 1.756 .57 .812
8 541 1045 490 880 51 165 507 915 11 16 2.588 225 720 1.143 .451 31 48 188 205 0 1055 888 167 3.275 .305 1.711
9 512 866 499 857 13 9 509 882 2 8 2.394 225 720 .465 .177 31 48 205 222 0 874 865 9 .692 1.444 -.531
10 536 991 499 872 37 119 505 895 7 13 2.5 225 731 .809 .312 31 48 223 240 0 1001 880 121 3.27 .306 1.709
11 494 920 479 903 15 17 489 931 2 9 3.143 225 745 .216 .075 31 48 240 257 0 929 912 17 1.133 .882 .181
12 494 909 467 832 27 77 477 848 5 11 2.552 225 756 .573 .465 31 48 258 275 0 918 840 78 2.889 .346 1.531
13 184 344 195 315 null 29 326 530 17 20 1.866 225 746 .803 .601 31 48 275 292 0 347 318 29 null null null
14 112 189 120 199 null null 154 239 8 13 1.908 225 756 .799 .51 31 48 293 310 0 190 201 null null null null
15 80 167 116 212 null null 192 301 3 8 1.833 225 756 1.124 .735 31 48 310 327 0 168 214 null null null null
16 106 181 133 254 null null 248 380 3 4 2.664 225 756 1.197 .826 31 48 328 345 0 182 256 null null null null
17 96 180 295 397 null null 294 477 0 0 null 225 756 1.297 .826 31 48 345 362 0 181 401 null null null null
18 224 433 409 626 null null 483 862 11 12 2.017 225 756 1.769 .949 31 48 363 380 -100 437 632 null null null null
19 513 930 417 698 96 232 530 955 16 22 2.819 225 756 1.809 .894 31 48 380 397 0 939 705 234 2.438 .41 1.285
20 420 659 400 680 20 null 414 717 4 8 3.336 225 720 .661 .24 32 49 398 415 0 665 686 null null null null

Total number of rows: 8064

Table truncated, full table size 923 Kbytes.




Supplementary data files not provided

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