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Sample GSM65089 Query DataSets for GSM65089
Status Public on Jul 22, 2005
Title trr - 0.1 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/2000-06/6679.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 1656 1825 514 361 1142 1464 545 403 56 62 1.155 225 990 1.237 .912 111 128 88 105 0 2198 434 1764 1.545 .647 .627
2 793 1002 468 368 325 634 490 417 16 23 1.414 225 741 1.614 .776 110 127 105 122 0 1207 443 764 2.351 .425 1.233
3 1736 1863 486 359 1250 1504 509 406 56 58 1.051 225 756 1.217 .932 110 127 122 139 0 2244 432 1812 1.45 .69 .536
4 937 932 520 331 417 601 542 369 20 28 1.483 225 756 1.372 .94 110 127 140 157 0 1122 398 724 1.736 .576 .796
5 1036 1010 539 325 497 685 553 359 31 39 1.359 225 756 1.352 .953 110 127 157 174 0 1216 391 825 1.66 .602 .731
6 820 813 533 320 287 493 549 366 14 28 1.843 225 756 1.44 .927 110 127 175 192 0 979 385 594 2.07 .483 1.049
7 1445 1395 525 325 920 1070 546 386 44 53 1.035 225 746 1.152 .949 110 127 192 209 0 1680 391 1289 1.401 .714 .487
8 556 406 512 349 44 57 550 448 7 19 .883 225 756 1.522 .696 110 127 210 227 0 489 420 69 1.568 .638 .649
9 545 358 512 347 33 11 546 434 6 9 .971 225 730 2.14 .812 110 127 227 244 0 431 418 13 .394 2.538 -1.344
10 550 363 518 331 32 32 535 369 4 14 1.222 225 731 .773 .511 110 127 244 261 0 437 398 39 1.219 .821 .285
11 553 383 507 333 46 50 539 429 9 17 .966 225 720 2.483 .71 110 127 262 279 0 461 401 60 1.304 .767 .383
12 556 374 510 311 46 63 538 402 8 19 1.194 225 720 2.425 .671 110 127 279 296 0 450 374 76 1.652 .605 .724
13 563 344 535 328 28 16 1197 1008 3 12 1.126 225 720 .889 .924 110 127 297 314 0 414 395 19 .679 1.474 -.559
14 558 363 548 356 10 7 1225 1036 4 15 .937 225 709 .889 .924 110 127 314 331 0 437 428 9 .9 1.111 -.152
15 608 395 548 349 60 46 1208 1007 5 10 .981 225 720 .89 .924 110 127 332 349 0 475 420 55 .917 1.091 -.126
16 576 325 515 312 61 13 547 357 6 14 .982 225 705 .331 .444 110 127 349 366 0 391 375 16 .262 3.813 -1.931
17 589 385 534 294 55 91 566 344 6 20 1.228 225 720 .912 .714 110 127 366 383 0 463 354 109 1.982 .505 .987
18 758 521 553 294 205 227 590 351 22 36 1.096 225 720 .689 .541 110 127 384 401 0 627 354 273 1.332 .751 .413
19 565 330 542 300 23 30 575 349 4 20 1.148 225 720 .559 .479 110 127 401 418 0 397 361 36 1.565 .639 .646
20 546 348 527 304 19 44 677 623 3 15 1.309 225 756 1.202 .78 109 126 419 436 0 419 366 53 2.789 .358 1.48

Total number of rows: 8064

Table truncated, full table size 923 Kbytes.




Supplementary data files not provided

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