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Sample GSM84136 Query DataSets for GSM84136
Status Public on Nov 19, 2005
Title 072801 100% CD28 beads 02.00 hr. T-Cell
Sample type RNA
 
Channel 1
Source name 10 amplified MOATS pool
Organism Homo sapiens
Characteristics 10 amplified MOATS pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 072801 100% CD28 beads 02.00 hr.
Organism Homo sapiens
Characteristics 072801 100% CD28 beads 02.00 hr.
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: T-cell, Costimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18932.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 Nov 17, 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 GPL3093
Series (1)
GSE3630 T-cell co-stimulation

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 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
1 2408 1267 170 695 2238 572 1604 1144 181 728 1434 449 0 0 1838 586 79 305 100 65 98 38 2810 1883 3.913 .256 .313 .333 .35 2.297 80 533 .217 .57 110 1630 8920 45 56 36 47 0 3017 1655 1362 .609 2724 1069 1.643 .746 -.717 -.424
2 902 1343 174 688 728 655 934 1342 195 727 760 654 0 0 284 443 84 299 100 84 100 50 1383 1414 1.111 .9 .861 .88 .999 2.062 32 109 1.737 .55 60 1800 8900 46 52 56 62 0 3198 1638 1560 2.142 3195 1557 .467 2.049 1.099 1.035
3 2389 1941 163 668 2226 1273 1972 1717 198 713 1809 1049 0 0 1362 863 168 341 100 86 100 71 3499 2858 1.749 .572 .58 .521 .532 1.838 52 275 .603 .82 90 1940 8890 43 52 68 77 0 4621 1590 3031 1.362 4088 2498 .734 1.381 .445 .465
4 2490 1449 164 647 2326 802 2253 1427 196 692 2089 780 0 0 1198 634 150 325 100 75 100 51 3128 2869 2.9 .345 .373 .319 .336 2.145 52 335 .335 .69 90 2100 8910 45 54 84 93 0 3450 1540 1910 .821 3398 1857 1.218 .889 -.285 -.17
5 2734 1383 397 820 2337 563 2886 1153 415 810 2489 333 0 0 827 439 229 274 100 75 100 33 2900 2822 4.151 .241 .134 .197 .137 2.573 12 30 .187 .4 40 2260 8890 46 50 103 107 0 3293 1952 1340 .574 2745 793 1.743 .319 -.802 -1.65
6 10025 1503 161 738 9864 765 7851 1350 183 733 7690 612 0 0 6687 633 107 290 100 73 100 51 10629 8302 12.894 .078 .08 .08 .082 2.021 80 336 .068 .7 100 2410 8900 44 54 115 125 0 3579 1757 1821 .185 3214 1457 5.416 .189 -2.437 -2.4
7 272 800 164 701 108 99 185 712 181 727 21 11 0 0 199 403 237 287 17 25 8 11 207 32 1.091 .917 .524 2.472 1.736 5.346 80 310 5.816 .39 100 2560 8930 47 57 130 140 -50 1905 1669 236 2.183 1695 26 .458 1.247 1.126 .319
8 7304 1831 161 670 7143 1161 6700 1694 184 713 6539 1024 0 0 3673 844 213 309 100 88 100 71 8304 7563 6.152 .163 .157 .151 .147 1.968 80 421 .144 .73 110 2710 8890 42 53 144 155 0 4360 1595 2764 .387 4033 2438 2.584 .373 -1.37 -1.423
9 1458 1303 242 751 1216 552 1541 1216 291 819 1299 465 0 0 445 532 166 379 100 50 100 33 1768 1764 2.203 .454 .358 .425 .515 2.411 12 58 .507 .31 50 2860 8890 45 50 162 167 0 3102 1788 1314 1.081 2895 1107 .925 .852 .112 -.231
10 2185 1755 260 653 1925 1102 2200 1757 318 721 1940 1104 0 0 577 436 249 354 100 91 100 91 3027 3044 1.747 .572 .569 .542 .574 1.952 12 64 .522 .62 50 3020 8900 46 51 178 183 0 4179 1555 2624 1.363 4183 2629 .734 1.355 .447 .438
11 1449 1640 299 685 1150 955 1329 1614 347 813 1030 929 0 0 585 516 190 431 100 83 100 58 2105 1959 1.204 .83 .902 .765 .946 1.881 12 52 .896 .77 50 3180 8880 44 49 194 199 0 3905 1631 2274 1.977 3843 2212 .506 2.147 .983 1.103
12 1252 1648 163 646 1089 1002 1191 1699 183 709 1028 1053 0 0 609 587 84 301 96 84 96 68 2091 2081 1.087 .92 1.024 .848 .898 2.178 32 114 .969 .74 60 3350 8900 46 52 211 217 0 3924 1538 2386 2.191 4045 2507 .456 2.439 1.131 1.286
13 1204 1310 179 684 1025 626 1144 1234 225 716 965 550 0 0 631 455 139 275 96 75 87 50 1651 1515 1.637 .611 .57 .705 .679 2.185 32 99 .607 .55 60 3500 8890 45 51 226 232 0 3119 1629 1490 1.454 2938 1310 .688 1.357 .54 .44
14 3008 3864 159 710 2849 3154 1745 3004 183 741 1586 2294 0 0 2627 2538 99 315 100 95 98 83 6003 3880 .903 1.107 1.446 1.082 .955 2.304 80 460 1.056 .81 110 3650 8900 43 54 238 249 0 9200 1690 7510 2.636 7152 5462 .379 3.444 1.398 1.784
15 1577 1585 182 825 1395 760 1606 1424 237 860 1424 599 0 0 500 562 132 354 100 75 91 50 2155 2023 1.836 .545 .421 .402 .414 3.801 12 64 .735 .42 50 3830 8900 46 51 259 264 0 3774 1964 1810 1.297 3390 1426 .771 1.002 .375 .002
16 2597 1980 160 703 2437 1277 1555 1579 184 754 1395 876 0 0 2240 1127 296 318 98 82 92 63 3714 2271 1.908 .524 .628 .538 .519 1.977 80 479 .465 .82 110 3970 8900 43 54 270 281 0 4714 1674 3040 1.248 3760 2086 .802 1.495 .319 .58
17 1084 1460 220 726 864 734 1057 1425 263 798 837 699 0 0 366 362 137 344 100 91 91 50 1598 1536 1.177 .85 .835 .839 .635 2.224 12 58 1.39 .48 50 4130 8890 45 50 289 294 0 3476 1729 1748 2.023 3393 1664 .494 1.988 1.016 .992
18 1310 2068 197 693 1113 1375 1344 2261 216 785 1147 1568 0 0 317 498 94 331 100 100 100 91 2488 2715 .809 1.235 1.367 1.196 1.276 1.842 12 58 1.918 .58 50 4280 8890 45 50 304 309 0 4924 1650 3274 2.941 5383 3733 .34 3.255 1.557 1.703
19 1592 3389 159 656 1433 2733 1608 3188 169 705 1449 2532 0 0 807 1515 65 295 100 97 96 95 4166 3981 .524 1.907 1.747 2.003 1.84 2.112 80 391 2.14 .84 100 4430 8900 44 54 317 327 0 8069 1562 6507 4.541 7590 6029 .22 4.161 2.183 2.057
20 876 2172 177 722 699 1450 957 2069 191 796 780 1347 0 0 332 763 74 369 100 91 83 83 2149 2127 .482 2.074 1.727 2.656 2.457 1.827 12 64 2.539 .47 50 4590 8900 46 51 335 340 0 5171 1719 3452 4.939 4926 3207 .202 4.112 2.304 2.04

Total number of rows: 37632

Table truncated, full table size 8652 Kbytes.




Supplementary data files not provided
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