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Sample GSM65083 Query DataSets for GSM65083
Status Public on Jul 22, 2005
Title trr - 0.1 mM H2O2 - 30 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 = 30 min
Organism Saccharomyces cerevisiae
Characteristics time = 30 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6681.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 1233 960 398 145 835 815 402 153 57 64 .935 225 990 .933 .937 36 53 86 103 0 1333 201 1132 1.356 .738 .439
2 439 194 399 144 40 50 403 151 7 19 .82 225 741 .693 .671 35 52 103 120 0 269 200 69 1.725 .58 .787
3 998 735 395 142 603 593 400 151 56 65 .956 225 756 .874 .921 35 52 120 137 0 1020 197 823 1.365 .733 .449
4 499 237 398 144 101 93 402 155 15 26 .8 225 756 .665 .776 35 52 138 155 0 329 200 129 1.277 .783 .353
5 819 709 404 148 415 561 408 161 36 57 .97 225 731 1.536 .986 35 52 155 172 0 984 205 779 1.877 .533 .909
6 441 202 408 153 33 49 420 187 7 16 .737 225 756 1.264 .733 35 52 172 189 0 280 212 68 2.061 .485 1.043
7 815 485 397 151 418 334 411 181 45 51 .759 225 756 .878 .812 35 52 190 207 0 673 209 464 1.11 .901 .151
8 391 155 392 150 null 5 402 160 2 8 .507 225 746 .176 .225 35 52 207 224 0 215 208 7 null null null
9 409 156 399 145 10 11 406 152 1 14 .5 225 756 .146 .185 35 52 225 242 0 216 201 15 1.5 .667 .585
10 400 145 395 141 5 4 399 148 2 12 .605 225 741 .102 .157 35 52 242 259 0 201 195 6 1.2 .833 .263
11 391 145 394 140 null 5 397 147 0 9 .667 225 756 .093 .143 35 52 259 276 0 201 194 7 null null null
12 400 139 388 141 12 null 395 149 1 7 .415 225 756 .113 .157 35 52 277 294 0 193 195 null null null null
13 398 156 382 141 16 15 390 149 3 15 .764 225 746 .148 .183 35 52 294 311 0 216 195 21 1.313 .762 .392
14 388 142 376 143 12 null 383 151 3 11 .636 225 756 .108 .134 35 52 312 329 0 197 198 null null null null
15 384 150 376 139 8 11 379 144 2 15 .664 225 741 .005 .008 35 52 329 346 0 208 193 15 1.875 .533 .907
16 386 148 385 134 1 14 389 139 0 15 .6 225 756 .026 .042 35 52 346 363 0 205 186 19 19 .053 4.248
17 406 146 391 133 15 13 401 147 4 16 .625 225 756 .747 .545 35 52 364 381 0 202 184 18 1.2 .833 .263
18 395 137 389 138 6 null 401 156 2 11 .628 225 746 .819 .582 35 52 381 398 0 190 191 null null null null
19 384 136 393 138 null null 436 184 1 9 .718 225 756 .979 .935 35 52 399 416 0 188 191 null null null null
20 427 157 399 135 28 22 439 174 3 18 .95 225 741 .943 .95 35 52 416 433 0 218 187 31 1.107 .903 .147

Total number of rows: 8064

Table truncated, full table size 916 Kbytes.




Supplementary data files not provided

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