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Sample GSM65082 Query DataSets for GSM65082
Status Public on Jul 22, 2005
Title wt - 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/2000-06/6672.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 3315 2334 1173 319 2142 2015 1185 345 58 68 .924 225 990 .957 .983 81 98 87 104 0 3826 522 3304 1.542 .648 .625
2 1353 538 1181 327 172 211 1201 355 8 22 1 225 741 .731 .869 80 97 104 121 0 881 536 345 2.006 .499 1.004
3 2843 1799 1164 326 1679 1473 1189 350 51 64 .87 225 756 .861 .979 80 97 121 138 0 2949 534 2415 1.438 .695 .524
4 1583 723 1184 321 399 402 1207 349 12 25 .855 225 756 .773 .953 80 97 139 156 0 1185 526 659 1.652 .605 .724
5 1684 823 1192 331 492 492 1216 361 15 41 .991 225 756 .843 .921 80 97 156 173 0 1349 542 807 1.64 .61 .714
6 1462 576 1201 330 261 246 1222 363 7 17 .78 225 756 .776 .946 80 97 174 191 0 944 540 404 1.548 .646 .63
7 2900 1605 1203 331 1697 1274 1221 352 43 51 .725 225 756 .767 .967 80 97 191 208 0 2631 542 2089 1.231 .812 .3
8 1279 426 1212 330 67 96 1234 351 2 24 .955 225 756 .655 .787 80 97 209 226 0 698 540 158 2.358 .424 1.238
9 1215 362 1204 326 11 36 1225 351 0 16 .912 225 756 .146 .196 80 97 226 243 0 593 534 59 5.364 .186 2.423
10 1229 349 1195 325 34 24 1221 360 0 12 .734 225 756 .455 .481 80 97 244 261 0 572 532 40 1.176 .85 .234
11 1238 349 1203 317 35 32 1239 373 0 15 .725 225 756 .617 .538 80 97 261 278 0 572 519 53 1.514 .66 .599
12 1236 322 1208 311 28 11 1258 366 0 12 .75 225 756 .587 .573 80 97 279 296 0 527 509 18 .643 1.556 -.637
13 1240 350 1236 315 4 35 1280 349 0 20 .662 225 756 .384 .555 80 97 296 313 0 573 516 57 14.25 .07 3.833
14 1289 361 1254 314 35 47 1285 334 1 15 .579 225 756 .744 .712 80 97 314 331 0 591 514 77 2.2 .455 1.138
15 1281 324 1262 305 19 19 1267 324 0 12 .705 225 756 .142 .226 80 97 331 348 0 531 500 31 1.632 .613 .706
16 1254 339 1231 307 23 32 1237 329 0 15 .668 225 756 .117 .177 80 97 349 366 0 555 503 52 2.261 .442 1.177
17 1216 424 1181 310 35 114 1202 331 1 16 .774 225 756 1.371 .712 80 97 366 383 0 695 508 187 5.343 .187 2.418
18 1131 316 1131 314 null 2 1148 336 1 7 .486 225 756 .079 .126 80 97 384 401 0 518 514 4 null null null
19 1105 349 1090 342 15 7 1111 371 0 9 .554 225 735 .119 .148 80 97 401 418 0 572 560 12 .8 1.25 -.322
20 1097 390 1112 345 null 45 1131 372 0 15 1.152 225 730 .124 .152 80 97 419 436 0 639 565 74 null null null

Total number of rows: 8064

Table truncated, full table size 936 Kbytes.




Supplementary data files not provided
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