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Sample GSM89762 Query DataSets for GSM89762
Status Public on Dec 29, 2005
Title Jurkat 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 Jurkat 0 hours, #2
Organism Homo sapiens
Characteristics Jurkat 0 hours, #2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stimulation, Jurkat cells
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14920.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
1 797 533 197 111 600 422 843 511 201 116 646 400 0 0 249 199 57 48 100 99 97 96 1022 1046 1.422 .703 .619 .702 .691 1.443 120 643 .707 .91 130 1810 8710 33 46 14 27 0 567 118 449 .748 544 426 1.336 .659 -.418 -.602 -.602
2 1271 1441 198 114 1073 1327 1228 1402 206 122 1030 1288 0 0 322 635 61 60 100 100 100 100 2400 2318 .809 1.237 1.25 1.147 1.193 1.401 80 319 1.356 .93 110 1960 8710 34 45 30 41 0 1533 121 1412 1.316 1491 1370 .76 1.33 .396 .412 .412
3 2504 5259 199 115 2305 5144 2447 5057 213 133 2248 4942 0 0 662 1916 79 106 100 100 100 100 7449 7190 .448 2.232 2.198 2.161 2.167 1.26 80 290 2.37 .97 110 2090 8720 35 46 43 54 0 5595 122 5472 2.374 5380 5257 .421 2.339 1.247 1.226 1.226
4 899 791 199 110 700 681 878 755 208 126 679 645 0 0 299 363 69 94 99 98 98 92 1381 1324 1.028 .973 .95 .927 .922 1.446 120 384 1.04 .92 120 2230 8710 34 46 57 69 0 841 117 724 1.035 803 686 .966 1.011 .05 .015 .015
5 975 722 204 113 771 609 971 738 214 124 767 625 0 0 191 254 67 51 100 100 100 98 1380 1392 1.266 .79 .815 .734 .811 1.669 80 308 .798 .84 110 2360 8710 34 45 70 81 0 768 120 648 .84 785 665 1.19 .867 -.251 -.206 -.206
6 993 570 200 113 793 457 990 568 212 125 790 455 0 0 159 147 69 51 100 100 100 100 1250 1245 1.735 .576 .576 .553 .572 1.475 80 337 .53 .85 110 2500 8710 34 45 84 95 0 606 120 486 .613 604 484 1.631 .613 -.706 -.707 -.707
7 1543 1883 197 113 1346 1770 1644 1977 200 117 1447 1864 0 0 488 601 56 39 99 100 99 100 3116 3311 .76 1.315 1.288 1.339 1.307 1.294 120 401 1.308 .97 120 2640 8710 34 46 98 110 0 2003 120 1883 1.399 2103 1983 .715 1.37 .484 .455 .455
8 994 640 199 114 795 526 997 608 199 117 798 494 0 0 212 225 48 36 98 100 98 100 1321 1292 1.511 .662 .619 .641 .63 1.461 80 433 .671 .9 110 2770 8700 33 44 111 122 0 681 121 560 .704 647 526 1.421 .659 -.507 -.603 -.603
9 689 343 192 109 497 234 685 338 196 114 493 229 0 0 143 83 45 38 100 100 100 98 731 722 2.124 .471 .465 .458 .487 1.525 80 463 .443 .85 110 3070 8690 32 43 141 152 0 365 116 249 .501 360 244 1.996 .494 -.997 -1.017 -1.017
10 1679 2993 200 119 1479 2874 1719 2808 209 139 1519 2689 0 0 402 1108 60 78 100 100 100 100 4353 4208 .515 1.943 1.77 1.85 1.867 1.309 80 416 2.077 .96 110 3230 8680 31 42 157 168 0 3184 127 3057 2.067 2987 2861 .484 1.883 1.048 .913 .913
11 1684 3822 197 120 1487 3702 1762 3828 206 136 1565 3708 0 0 829 2166 58 75 98 100 97 100 5189 5273 .402 2.49 2.369 2.414 2.513 1.508 120 464 2.599 .97 120 3390 8680 31 43 173 185 0 4066 128 3938 2.648 4072 3945 .378 2.521 1.405 1.334 1.334
12 745 598 196 114 549 484 741 601 197 117 545 487 0 0 147 179 47 36 100 100 100 97 1033 1032 1.134 .882 .894 .834 .875 1.495 80 356 .88 .89 100 3540 8680 32 42 189 199 0 636 121 515 .938 639 518 1.066 .951 -.093 -.073 -.073
13 874 736 196 113 678 623 892 705 201 118 696 592 0 0 181 223 46 37 100 100 100 100 1301 1288 1.088 .919 .851 .89 .913 1.404 80 435 .91 .91 110 3710 8680 31 42 205 216 0 783 120 663 .978 750 630 1.023 .905 -.033 -.144 -.144
14 818 405 195 112 623 293 824 396 198 116 629 284 0 0 142 110 46 35 100 100 100 98 916 913 2.126 .47 .452 .447 .465 1.532 80 381 .452 .87 110 3870 8680 31 42 221 232 0 431 119 312 .5 421 302 1.999 .48 -.999 -1.058 -1.058
15 720 855 191 110 529 745 682 829 194 113 491 719 0 0 261 335 44 32 99 100 99 100 1274 1210 .71 1.408 1.464 1.413 1.464 1.432 120 390 1.405 .92 120 4020 8680 31 43 236 248 0 910 117 793 1.498 882 765 .667 1.558 .583 .64 .64
16 734 554 192 113 542 441 751 540 194 115 559 427 0 0 255 275 45 34 97 95 95 93 983 986 1.229 .814 .764 .754 .78 1.815 120 393 .876 .9 120 4170 8670 30 42 251 263 0 589 120 469 .866 574 454 1.155 .813 -.208 -.299 -.299
17 1026 654 193 113 833 541 1020 639 196 117 827 526 0 0 395 252 45 37 99 98 98 97 1374 1353 1.54 .649 .636 .65 .641 1.548 120 423 .621 .92 120 4330 8680 31 43 267 279 0 696 120 576 .691 680 560 1.447 .677 -.533 -.564 -.564
18 1542 2273 192 115 1350 2158 1542 2214 194 122 1350 2099 0 0 375 668 47 59 100 100 100 100 3508 3449 .626 1.599 1.555 1.587 1.595 1.208 80 420 1.637 .97 110 4480 8670 30 41 282 293 0 2418 122 2296 1.701 2355 2233 .588 1.654 .766 .726 .726
19 1503 2542 196 118 1307 2424 1491 2534 234 126 1295 2416 0 0 378 711 437 64 100 100 83 100 3731 3711 .539 1.855 1.866 1.855 1.801 1.209 80 373 1.667 .77 110 4650 8680 31 42 299 310 0 2704 126 2579 1.973 2696 2570 .507 1.985 .98 .989 .989
20 1993 3010 206 117 1787 2893 1899 2714 515 187 1693 2597 0 0 877 1405 2853 678 13 95 0 89 4680 4290 .618 1.619 1.534 1.635 1.641 1.333 120 414 .353 .66 120 4800 8670 30 42 314 326 0 3202 124 3078 1.722 2887 2763 .581 1.632 .784 .707 .707

Total number of rows: 37632

Table truncated, full table size 8517 Kbytes.




Supplementary data files not provided
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