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Sample GSM130498 Query DataSets for GSM130498
Status Public on Aug 25, 2006
Title Lung_6508
Sample type RNA
 
Channel 1
Source name Amplified universal human reference
Organism Homo sapiens
Characteristics Amplified universal human reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name clonetic lung fibroblasts #6508
Organism Homo sapiens
Characteristics clonetic lung fibroblasts #6508
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59455.gif; format: 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 Aug 24, 2006
Last update date Aug 24, 2006
Contact name Howard Chang
E-mail(s) [email protected]
Fax 650-723-8762
Organization name Stanford University
Department Dermatology
Street address CCSR 2142
City Stanford
State/province CA
Country USA
 
Platform ID GPL4214
Series (1)
GSE5591 Anatomic demarcation by positional variation in fibroblast gene expression programs.

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 2026 1447 560 723 1466 724 2361 1521 565 742 1801 798 0 0 909 420 130 141 78 92 76 78 2190 2599 2.025 .494 .443 .478 .465 1.913 52 286 .437 .87 80 1740 4940 58 66 42 50 0 2196 1097 1099 .75 2308 1211 1.334 .672 -.416 -.572
2 9403 2684 576 770 8827 1914 11340 3066 583 773 10764 2296 0 0 4743 913 138 156 94 92 94 88 10741 13060 4.612 .217 .213 .256 .214 1.705 52 265 .197 .97 80 1880 4950 59 67 56 64 0 4073 1169 2905 .329 4653 3485 3.039 .324 -1.603 -1.627
3 2789 1582 552 757 2237 825 3088 1562 616 780 2536 805 0 0 1406 423 356 194 81 90 71 81 3062 3341 2.712 .369 .317 .449 .398 1.833 32 213 .325 .9 70 2030 4940 58 65 71 78 0 2401 1149 1252 .56 2371 1222 1.787 .482 -.837 -1.054
4 2578 1433 545 746 2033 687 3155 1574 579 760 2610 828 0 0 1283 465 257 159 78 76 75 73 2720 3438 2.959 .338 .317 .367 .325 2.023 52 276 .332 .91 80 2170 4940 58 66 85 93 0 2175 1132 1043 .513 2389 1257 1.95 .481 -.963 -1.054
5 2863 2858 551 746 2312 2112 3288 3295 570 750 2737 2549 0 0 1251 1052 140 139 82 90 80 88 4424 5286 1.095 .913 .931 1.16 .93 2.203 52 276 .871 .96 80 2320 4940 58 66 100 108 0 4338 1132 3205 1.386 5001 3869 .721 1.413 .471 .499
6 1484 1155 562 746 922 409 1648 1189 582 742 1086 443 0 0 668 304 164 143 75 71 71 68 1331 1529 2.254 .444 .408 .469 .422 1.855 32 219 .437 .85 70 2460 4940 58 65 114 121 0 1753 1132 621 .673 1805 672 1.485 .619 -.571 -.692
7 1970 1850 569 754 1401 1096 2288 2032 594 757 1719 1278 0 0 824 527 213 179 78 93 75 87 2497 2997 1.278 .782 .743 .953 .776 1.8 32 225 .754 .93 70 2610 4940 58 65 129 136 0 2808 1144 1663 1.187 3084 1940 .842 1.128 .248 .174
8 2890 3130 570 759 2320 2371 3429 3521 580 770 2859 2762 0 0 1505 1371 163 155 82 92 78 86 4691 5621 .978 1.022 .966 1.204 1.011 2.509 52 264 .971 .96 80 2760 4940 58 66 144 152 0 4750 1152 3598 1.551 5344 4192 .645 1.466 .633 .552
9 3818 1758 560 755 3258 1003 4263 1863 614 774 3703 1108 0 0 1705 532 340 170 84 90 80 82 4261 4811 3.248 .308 .299 .344 .312 2.04 52 301 .278 .92 90 2900 4940 57 66 157 166 0 2668 1146 1522 .467 2827 1682 2.14 .454 -1.098 -1.139
10 7110 3575 583 775 6527 2800 7795 3732 652 786 7212 2957 0 0 2566 903 413 185 96 100 90 100 9327 10169 2.331 .429 .41 .491 .425 1.687 52 300 .39 .96 90 3050 4940 57 66 172 181 0 5426 1176 4249 .651 5664 4488 1.536 .622 -.619 -.684
11 7123 9926 569 782 6554 9144 8172 11153 652 844 7603 10371 0 0 3116 3596 583 495 86 96 86 94 15698 17974 .717 1.395 1.364 1.705 1.365 2.31 52 312 1.288 .97 90 3190 4940 57 66 186 195 0 15064 1187 13878 2.117 16927 15740 .472 2.07 1.082 1.05
12 20124 18842 574 755 19550 18087 25850 22845 627 817 25276 22090 0 0 11555 9143 495 461 96 98 83 91 37637 47366 1.081 .925 .874 1.132 .926 1.79 80 385 .87 .98 100 3350 4940 57 67 202 212 0 28596 1146 27450 1.404 34671 33525 .712 1.326 .49 .407
13 5358 10812 575 760 4783 10052 6242 12293 653 884 5667 11533 0 0 2343 4139 587 757 84 90 82 88 14835 17200 .476 2.102 2.035 2.482 2.1 1.88 52 289 1.964 .98 90 3490 4930 56 65 216 225 0 16409 1153 15256 3.19 18657 17503 .314 3.089 1.673 1.627
14 2805 1855 544 776 2261 1079 3053 1939 617 849 2509 1163 0 0 1020 433 540 663 87 85 82 33 3340 3672 2.095 .477 .464 .534 .487 1.917 80 370 .476 .89 100 3640 4940 57 67 231 241 0 2815 1178 1638 .724 2943 1765 1.381 .703 -.465 -.507
15 2276 1582 572 760 1704 822 2445 1606 695 823 1873 846 0 0 867 298 657 303 80 92 78 82 2526 2719 2.073 .482 .452 .622 .455 2.597 52 289 .393 .89 90 3780 4930 56 65 245 254 0 2401 1153 1248 .732 2437 1284 1.366 .686 -.45 -.545
16 15933 10813 571 779 15362 10034 18222 12035 665 812 17651 11256 0 0 7284 4501 561 275 90 98 86 95 25396 28907 1.531 .653 .638 .753 .653 1.649 80 362 .628 .97 100 3930 4940 57 67 260 270 0 16411 1182 15228 .991 18265 17083 1.009 .968 -.013 -.047
17 10907 7455 545 747 10362 6708 13113 8516 699 827 12568 7769 0 0 5603 3330 1208 603 80 86 80 82 17070 20337 1.545 .647 .618 .748 .644 1.714 52 300 .599 .97 90 4070 4930 56 65 274 283 0 11314 1134 10181 .982 12925 11791 1.018 .938 -.025 -.092
18 4601 2378 546 741 4055 1637 5007 2405 692 824 4461 1664 0 0 1506 525 1199 598 90 94 84 82 5692 6125 2.477 .404 .373 .446 .407 1.625 52 302 .377 .94 90 4220 4940 57 66 289 298 0 3609 1125 2484 .613 3650 2525 1.632 .566 -.707 -.821
19 13530 9326 548 727 12982 8599 16519 11051 1029 1038 15971 10324 0 0 7229 4440 2555 1712 78 80 78 78 21581 26295 1.51 .662 .646 .813 .674 1.632 52 313 .635 .97 90 4360 4930 56 65 303 312 0 14154 1103 13050 1.005 16772 15668 .995 .981 .008 -.028
20 18246 10401 557 745 17689 9656 21136 11534 1337 1169 20579 10789 0 0 7360 3326 3212 1855 88 96 84 88 27345 31368 1.832 .546 .524 .624 .538 1.553 52 312 .505 .97 90 4510 4930 56 65 318 327 0 15785 1131 14655 .828 17505 16374 1.207 .796 -.271 -.33

Total number of rows: 41472

Table truncated, full table size 9668 Kbytes.




Supplementary data files not provided
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