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Sample GSM89753 Query DataSets for GSM89753
Status Public on Dec 29, 2005
Title J14 SLP-76 negative 0 hours, #3
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name J14 SLP-76 negative 0 hours
Organism Homo sapiens
Characteristics J14 SLP-76 negative 0 hours
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stimulation, Jurkat cells
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16222.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 2383 1373 1004 360 1379 1013 2385 1363 1000 378 1381 1003 0 0 463 383 162 132 100 98 100 97 2392 2384 1.361 .735 .726 .71 .701 1.635 80 454 .7 .87 110 1750 8280 15 26 44 55 0 995 261 734 .532 988 727 1.879 .526 -.91 -.926 -.926
2 2747 3476 985 389 1762 3087 2759 3427 1006 402 1774 3038 0 0 530 1282 178 134 100 100 100 100 4849 4812 .571 1.752 1.713 1.691 1.727 1.453 80 316 1.887 .9 110 1900 8280 15 26 59 70 0 2519 282 2237 1.27 2483 2201 .788 1.241 .344 .311 .311
3 3429 6501 1019 380 2410 6121 3438 6294 1019 387 2419 5914 0 0 1174 3331 171 123 100 100 97 100 8531 8333 .394 2.54 2.445 2.448 2.474 1.35 120 325 2.703 .95 120 2030 8300 17 29 72 84 0 4711 275 4436 1.84 4561 4286 .543 1.772 .88 .825 .825
4 2449 1640 1028 359 1421 1281 2459 1605 1017 374 1431 1246 0 0 563 708 172 124 100 100 100 96 2702 2677 1.109 .901 .871 .828 .843 1.565 80 296 .931 .86 110 2170 8280 15 26 86 97 0 1188 260 928 .653 1163 903 1.531 .631 -.614 -.664 -.664
5 2344 1442 1003 377 1341 1065 2319 1424 1006 387 1316 1047 0 0 454 349 177 128 100 100 98 98 2406 2363 1.259 .794 .796 .803 .763 1.727 80 323 .725 .81 110 2300 8280 15 26 99 110 0 1045 273 772 .575 1032 759 1.738 .577 -.797 -.795 -.795
6 2640 1665 1008 414 1632 1251 2670 1598 1016 423 1662 1184 0 0 515 435 180 132 100 100 98 100 2883 2846 1.305 .767 .712 .763 .758 1.468 80 378 .739 .88 110 2440 8270 14 25 113 124 0 1207 300 907 .555 1158 858 1.8 .516 -.848 -.954 -.954
7 3255 2954 1005 428 2250 2526 3271 3095 1013 440 2266 2667 0 0 1049 1020 190 147 100 100 96 98 4776 4933 .891 1.123 1.177 1.154 1.124 1.477 80 379 1.069 .95 110 2570 8270 14 25 126 137 0 2141 310 1830 .814 2243 1933 1.229 .853 -.298 -.23 -.23
8 2254 1639 995 418 1259 1221 2264 1563 1008 430 1269 1145 0 0 565 587 183 143 98 100 92 100 2480 2414 1.031 .97 .902 .964 .997 1.612 80 485 .95 .87 110 2710 8260 13 24 140 151 0 1188 303 885 .703 1133 830 1.423 .654 -.509 -.613 -.613
9 1566 642 962 417 604 225 1529 636 978 427 567 219 0 0 261 170 173 137 96 77 87 32 829 786 2.684 .373 .386 .392 .407 2.75 80 422 .3 .44 100 3010 8270 15 25 171 181 0 465 302 163 .27 461 159 3.705 .28 -1.889 -1.837 -1.837
10 2686 3593 1004 448 1682 3145 2720 3481 1012 460 1716 3033 0 0 537 1144 177 146 98 100 98 100 4827 4749 .535 1.87 1.767 1.808 1.739 1.408 80 438 1.943 .91 110 3160 8280 15 26 185 196 0 2604 325 2279 1.355 2522 2198 .738 1.281 .438 .357 .357
11 3049 5708 1011 476 2038 5232 2966 5812 1019 487 1955 5336 0 0 664 1879 182 147 100 100 100 100 7270 7291 .39 2.567 2.729 2.516 2.442 1.284 80 394 2.678 .95 100 3330 8270 15 25 203 213 0 4136 345 3791 1.86 4212 3867 .538 1.978 .896 .984 .984
12 2012 1292 1015 476 997 816 2042 1217 1037 485 1027 741 0 0 376 454 216 147 98 94 92 90 1813 1768 1.222 .818 .722 .705 .783 2.014 52 334 .798 .7 90 3480 8260 14 23 218 227 0 936 345 591 .593 882 537 1.686 .523 -.754 -.936 -.936
13 2052 1201 993 435 1059 766 2049 1171 1010 441 1056 736 0 0 314 324 197 139 100 98 98 95 1825 1792 1.383 .723 .697 .685 .718 1.727 80 489 .67 .77 110 3650 8260 13 24 234 245 0 870 315 555 .524 849 533 1.908 .505 -.932 -.986 -.986
14 2133 1143 1005 449 1128 694 2118 1114 1023 460 1113 665 0 0 335 408 189 151 100 93 98 85 1822 1778 1.625 .615 .597 .547 .575 2.167 80 441 .618 .73 110 3810 8270 14 25 250 261 0 828 325 503 .446 807 482 2.243 .433 -1.165 -1.208 -1.208
15 2663 2447 1072 487 1591 1960 2750 2551 1091 508 1678 2064 0 0 550 802 212 172 100 100 100 98 3551 3742 .812 1.232 1.23 1.184 1.198 1.419 52 302 1.225 .91 90 3950 8250 13 22 265 274 0 1773 353 1420 .893 1849 1496 1.12 .891 -.164 -.166 -.166
16 2005 1141 1055 457 950 684 1957 1130 1083 480 902 673 0 0 345 336 220 155 100 96 97 82 1634 1575 1.389 .72 .746 .662 .659 1.721 80 385 .691 .79 100 4110 8280 16 26 281 291 0 827 331 496 .522 819 488 1.917 .541 -.939 -.887 -.887
17 2442 1532 1061 460 1381 1072 2439 1516 1069 470 1378 1056 0 0 518 417 192 135 97 100 97 97 2453 2434 1.288 .776 .766 .803 .746 1.708 80 420 .75 .84 110 4270 8270 14 25 296 307 0 1110 333 777 .562 1099 765 1.778 .555 -.83 -.849 -.849
18 2492 2666 1057 455 1435 2211 2491 2670 1061 465 1434 2215 0 0 741 869 190 169 95 100 92 100 3646 3649 .649 1.541 1.545 1.59 1.53 1.439 80 474 1.486 .92 110 4430 8260 13 24 312 323 0 1932 330 1602 1.116 1935 1605 .896 1.119 .159 .163 .163
19 2990 4045 1050 443 1940 3602 3169 4080 1059 456 2119 3637 0 0 977 1433 188 172 95 100 95 100 5542 5756 .539 1.857 1.716 1.997 1.895 1.553 80 385 1.753 .95 110 4600 8280 15 26 329 340 0 2931 321 2610 1.345 2957 2636 .743 1.244 .428 .315 .315
20 2795 4100 1015 440 1780 3660 2591 3651 1022 443 1576 3211 0 0 1049 1884 185 135 97 100 95 100 5440 4787 .486 2.056 2.037 2.168 2.081 1.456 120 422 2.013 .95 120 4740 8270 14 26 343 355 0 2971 319 2652 1.49 2646 2327 .671 1.476 .575 .562 .562

Total number of rows: 37632

Table truncated, full table size 8598 Kbytes.




Supplementary data files not provided
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