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Sample GSM130496 Query DataSets for GSM130496
Status Public on Aug 25, 2006
Title Aorta_5640
Sample type RNA
 
Channel 1
Source name Amplifiied Human Universal Reference
Organism Homo sapiens
Characteristics Amplifiied Human Universal Reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Clonetic cells aorta fibroblasts #5640
Organism Homo sapiens
Characteristics Clonetic cells aorta fibroblasts #5640
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59470.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
1 533 363 277 483 256 -120 529 320 283 489 252 -163 0 0 184 235 66 124 80 23 69 5 136 89 null null null 1.212 1.17 3.034 52 298 .848 .84 80 1750 5100 50 58 27 35 -50 426 567 -141 null 376 -191 null null null null
2 3019 461 309 522 2710 -61 3207 444 595 511 2898 -78 0 0 2213 150 1010 131 65 9 56 3 2649 2820 null null null .406 .373 4.034 32 213 -.045 -.67 70 1890 5100 50 57 41 48 0 541 613 -72 null 522 -92 null null null null
3 940 684 283 515 657 169 835 692 357 522 552 177 0 0 604 176 440 119 53 61 36 34 826 729 3.888 .257 .321 .492 .385 3.627 52 274 .178 .54 80 2040 5100 50 58 56 64 0 803 605 199 .302 813 208 3.31 .377 -1.727 -1.409
4 489 337 265 452 224 -115 461 275 279 465 196 -177 0 0 177 204 95 116 71 19 53 1 109 19 null null null 1.91 1.359 4.245 52 264 -.676 -.58 80 2180 5100 50 58 70 78 -50 396 531 -135 null 323 -208 null null null null
5 581 1648 249 429 332 1219 624 1720 260 442 375 1291 0 0 209 932 71 139 82 86 71 71 1551 1666 .272 3.672 3.443 3.085 3.423 1.968 52 301 4.343 .91 90 2330 5110 50 59 84 93 0 1936 504 1432 4.313 2020 1516 .232 4.044 2.109 2.016
6 383 311 251 432 132 -121 361 309 260 450 110 -123 0 0 135 154 62 141 59 3 48 0 11 -13 null null null 1.719 2.021 5.43 52 274 -1.611 -.57 80 2470 5100 50 58 99 107 -50 365 507 -142 null 363 -144 null null null null
7 569 922 254 441 315 481 570 919 286 463 316 478 0 0 242 412 168 146 65 71 46 65 796 794 .655 1.527 1.513 1.545 1.572 1.828 32 219 1.524 .76 70 2620 5100 50 57 114 121 0 1083 518 565 1.794 1079 561 .558 1.777 .843 .829
8 471 491 255 431 216 60 473 460 268 454 218 29 0 0 179 117 76 137 73 17 53 5 276 247 3.6 .278 .133 .413 .343 3.596 52 284 .264 .16 80 2770 5100 50 58 129 137 -50 577 506 70 .326 540 34 3.065 .156 -1.616 -2.678
9 1065 469 256 442 809 27 1141 441 276 451 885 -1 0 0 304 120 86 117 98 25 94 3 836 884 29.963 .033 null .168 .171 5.502 52 289 -.041 -.13 90 2920 5110 50 59 143 152 0 551 519 32 .039 518 -1 25.509 null -4.673 null
10 1147 620 265 441 882 179 1348 597 331 454 1083 156 0 0 613 138 260 109 73 71 67 32 1061 1239 4.927 .203 .144 .249 .194 3.632 52 289 .119 .48 90 3060 5100 49 58 157 166 0 728 518 210 .238 701 183 4.195 .169 -2.069 -2.563
11 1758 3811 258 455 1500 3356 2121 4743 314 486 1863 4288 0 0 1169 2413 244 236 68 78 65 72 4856 6151 .447 2.237 2.302 2.934 2.264 2.792 80 366 2.166 .97 100 3210 5100 49 59 172 182 0 4476 534 3942 2.628 5571 5037 .381 2.704 1.394 1.435
12 10834 11507 257 465 10577 11042 13807 14782 403 563 13550 14317 0 0 8243 7711 911 568 68 82 65 76 21619 27867 .958 1.044 1.057 1.412 1.076 1.813 80 331 .951 .97 100 3360 5100 49 59 187 197 0 13516 546 12970 1.226 17363 16817 .816 1.241 .294 .312
13 2239 4499 259 457 1980 4042 2980 5450 380 586 2721 4993 0 0 1479 2831 744 689 66 73 57 71 6022 7714 .49 2.041 1.835 2.101 1.977 2.386 80 352 2.066 .96 100 3500 5100 49 59 201 211 0 5284 537 4748 2.398 6402 5865 .417 2.155 1.262 1.108
14 913 622 249 430 664 192 927 618 294 505 678 188 0 0 199 116 275 576 98 1 73 0 856 866 3.458 .289 .277 .265 .293 2.204 52 279 .273 .52 90 3650 5110 50 59 216 225 0 731 505 226 .34 726 221 2.944 .326 -1.558 -1.618
15 748 712 253 422 495 290 847 702 286 438 594 280 0 0 292 210 149 128 80 76 76 53 785 874 1.707 .586 .471 .553 .582 2.386 52 289 .564 .83 90 3790 5100 49 58 230 239 0 836 496 341 .688 825 329 1.453 .554 -.539 -.853
16 14534 7608 248 419 14286 7189 18496 8857 490 512 18248 8438 0 0 10443 5047 1452 532 73 80 70 76 21475 26686 1.987 .503 .462 .68 .532 2.012 80 344 .468 .97 100 3940 5100 49 59 245 255 0 8936 492 8444 .591 10403 9911 1.692 .543 -.759 -.881
17 4348 3456 243 433 4105 3023 5428 4462 477 524 5185 4029 0 0 3295 2164 1313 569 65 72 58 68 7128 9214 1.358 .736 .777 1.005 .776 1.975 80 344 .674 .95 100 4080 5100 49 59 259 269 0 4059 509 3551 .865 5241 4732 1.156 .913 -.209 -.132
18 1034 502 252 422 782 80 1250 507 319 450 998 85 0 0 482 121 439 289 73 3 59 0 862 1083 9.775 .102 .085 .193 .137 4.914 52 301 .075 .28 90 4230 5100 49 58 274 283 0 590 496 94 .12 596 100 8.322 .1 -3.057 -3.321
19 6424 4386 260 432 6164 3954 7267 4453 286 444 7007 4021 0 0 3135 2018 150 131 93 97 90 95 10118 11028 1.559 .641 .574 .779 .641 1.846 80 347 .614 .97 100 4380 5110 50 60 289 299 0 5152 507 4644 .753 5230 4723 1.327 .674 -.408 -.569
20 5358 4326 262 439 5096 3887 6923 5465 376 507 6661 5026 0 0 3448 2455 714 435 72 77 71 76 8983 11687 1.311 .763 .755 .924 .771 1.75 80 399 .706 .98 110 4520 5100 48 59 302 313 0 5081 516 4566 .896 6419 5904 1.116 .886 -.159 -.174

Total number of rows: 41472

Table truncated, full table size 9293 Kbytes.




Supplementary data files not provided
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