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Sample GSM89764 Query DataSets for GSM89764
Status Public on Dec 29, 2005
Title JurkatNegative (Mock stim) 0 hours, #2
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name JurkatNegative (Mock stim) 0 hours
Organism Homo sapiens
Characteristics JurkatNegative (Mock stim) 0 hours
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stimulation, Jurkat cells
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16178.gif
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 Dec 28, 2005
Last update date Sep 28, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3084
Series (1)
GSE3922 T cell Basal Signaling

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; 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
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total 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
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; 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 The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; 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
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; 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
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN 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
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE UNF_VALUE
1 1685 1764 415 202 1270 1562 1581 1706 422 212 1166 1504 0 0 530 744 99 87 100 100 100 100 2832 2670 .813 1.23 1.29 1.175 1.22 1.387 80 460 1.248 .94 110 1960 8810 27 38 82 93 0 1470 168 1302 1.025 1422 1253 .976 1.075 .036 .104 .104
2 2138 3769 417 207 1721 3562 2132 3811 425 226 1715 3604 0 0 802 1621 100 106 96 100 95 98 5283 5319 .483 2.07 2.101 2.081 2.046 1.435 120 415 2.106 .95 120 2090 8810 27 39 95 107 0 3141 173 2968 1.725 3176 3003 .58 1.751 .786 .808 .808
3 2335 4418 402 216 1933 4202 2406 4688 416 246 2004 4472 0 0 1009 1970 98 118 96 100 95 100 6135 6476 .46 2.174 2.232 2.233 2.178 1.447 120 369 2.168 .95 120 2240 8820 28 40 110 122 0 3682 180 3502 1.812 3907 3727 .552 1.86 .857 .895 .895
4 2012 2588 427 218 1585 2370 1991 2558 433 251 1564 2340 0 0 563 793 103 127 98 100 98 100 3955 3904 .669 1.495 1.496 1.506 1.447 1.335 80 341 1.473 .94 110 2370 8800 26 37 123 134 0 2157 182 1975 1.246 2132 1950 .803 1.247 .317 .318 .318
5 2211 3132 427 203 1784 2929 2290 3193 430 220 1863 2990 0 0 493 793 101 101 100 100 100 100 4713 4853 .609 1.642 1.605 1.653 1.598 1.328 80 342 1.64 .94 110 2510 8810 27 38 137 148 0 2610 169 2441 1.368 2661 2492 .731 1.337 .452 .419 .419
6 1731 2265 427 194 1304 2071 1844 2440 433 209 1417 2246 0 0 679 1152 104 82 88 92 85 90 3375 3663 .63 1.588 1.585 1.592 1.541 1.579 120 447 1.646 .94 120 2650 8800 26 38 151 163 0 1888 162 1726 1.323 2033 1872 .756 1.321 .404 .401 .401
7 2305 4064 439 202 1866 3862 2100 3869 442 213 1661 3667 0 0 835 1554 104 84 98 100 98 100 5728 5328 .483 2.07 2.208 2.094 2.023 1.295 80 356 1.974 .96 110 2780 8810 27 38 164 175 0 3387 168 3218 1.725 3224 3056 .58 1.84 .786 .88 .88
8 1706 2087 425 198 1281 1889 1648 1871 431 211 1223 1673 0 0 569 1023 89 76 98 100 98 98 3170 2896 .678 1.475 1.368 1.412 1.395 1.744 80 478 1.512 .91 110 2920 8810 27 38 178 189 0 1739 165 1574 1.229 1559 1394 .814 1.14 .297 .189 .189
9 1219 1177 420 216 799 961 1141 984 427 225 721 768 0 0 417 690 95 76 100 98 97 96 1760 1489 .831 1.203 1.065 1.048 1.051 2.022 80 486 1.357 .85 110 3230 8820 28 39 209 220 0 981 180 801 1.002 820 640 .998 .888 .003 -.172 -.172
10 2336 5389 432 219 1904 5170 2349 5357 440 235 1917 5138 0 0 548 1423 112 95 100 100 100 100 7074 7055 .368 2.715 2.68 2.723 2.668 1.288 80 457 2.732 .96 110 3380 8810 27 38 224 235 0 4491 183 4308 2.263 4464 4282 .442 2.234 1.178 1.159 1.159
11 2212 5148 432 218 1780 4930 2172 5093 441 235 1740 4875 0 0 639 1622 109 95 100 100 100 100 6710 6615 .361 2.77 2.802 2.806 2.805 1.279 80 417 2.779 .96 110 3550 8820 28 39 241 252 0 4290 182 4108 2.308 4244 4063 .433 2.335 1.207 1.223 1.223
12 1524 1868 436 206 1088 1662 1455 1711 445 214 1019 1505 0 0 496 955 100 79 100 100 97 100 2750 2524 .655 1.528 1.477 1.415 1.409 1.515 80 402 1.652 .9 110 3700 8820 28 39 256 267 0 1557 172 1385 1.273 1426 1254 .786 1.231 .348 .3 .3
13 1668 1995 423 199 1245 1796 1600 1809 429 208 1177 1610 0 0 537 906 96 79 100 100 98 100 3041 2787 .693 1.443 1.368 1.407 1.404 1.447 80 424 1.497 .91 110 3860 8820 28 39 272 283 0 1663 166 1497 1.202 1508 1342 .832 1.14 .266 .189 .189
14 1483 1348 427 212 1056 1136 1483 1223 437 222 1056 1011 0 0 420 588 97 81 97 100 97 100 2192 2067 .93 1.076 .957 .979 1.002 1.484 80 407 1.095 .87 110 4030 8820 28 39 289 300 0 1123 177 947 .896 1019 843 1.115 .798 -.158 -.326 -.326
15 2236 3602 441 214 1795 3388 2184 3495 446 224 1743 3281 0 0 852 1477 101 76 100 100 100 100 5183 5024 .53 1.887 1.882 1.939 1.86 1.317 80 405 1.829 .96 110 4180 8810 27 38 304 315 0 3002 178 2823 1.573 2913 2734 .636 1.569 .653 .65 .65
16 1659 2207 422 203 1237 2004 1571 2040 435 212 1149 1837 0 0 417 790 101 77 100 100 100 100 3241 2986 .617 1.62 1.599 1.584 1.589 1.364 80 344 1.666 .93 110 4340 8820 28 39 320 331 0 1839 169 1670 1.35 1700 1531 .741 1.332 .433 .414 .414
17 1797 2396 441 209 1356 2187 1840 2524 647 736 1399 2315 0 0 695 1016 667 1479 82 76 53 20 3543 3714 .62 1.613 1.655 1.743 1.734 1.627 120 415 2.014 .91 120 4490 8820 28 40 335 347 0 1997 174 1823 1.344 2103 1929 .744 1.379 .427 .464 .464
18 1543 2371 412 193 1131 2178 1530 2232 589 635 1118 2039 0 0 592 963 616 1386 84 82 43 24 3309 3157 .519 1.926 1.824 2.027 1.88 1.636 120 469 2.129 .94 120 4650 8810 27 39 351 363 0 1976 161 1815 1.605 1860 1699 .623 1.52 .682 .604 .604
19 2647 5217 394 190 2253 5027 2569 5086 407 206 2175 4896 0 0 874 1605 101 130 98 100 98 100 7280 7071 .448 2.231 2.251 2.264 2.21 1.236 80 394 2.119 .95 110 4810 8820 28 39 367 378 0 4348 158 4189 1.859 4238 4080 .538 1.876 .895 .908 .908
20 2266 3922 409 202 1857 3720 2157 3573 425 230 1748 3371 0 0 1004 1696 127 154 98 100 96 100 5577 5119 .499 2.003 1.928 2.085 1.954 1.405 80 428 2.014 .94 110 4970 8810 27 38 383 394 0 3268 168 3100 1.669 2978 2809 .599 1.607 .739 .684 .684

Total number of rows: 37632

Table truncated, full table size 8576 Kbytes.




Supplementary data files not provided
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