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Sample GSM253401 Query DataSets for GSM253401
Status Public on Mar 01, 2008
Title H1155
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name H1155; LC (8170s1)
Organism Homo sapiens
Characteristics H1155; LC (8170s1)
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: aCGH, Lung Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38008.gif
Cell Line: H1155
The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.
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 26, 2007
Last update date Jan 11, 2008
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL6322
Series (2)
GSE9995 Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer
GSE10025 Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer: aCGH Arrays

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 1098 773 374 375 724 398 1171 676 383 383 797 301 0 0 357 260 88 111 100 93 93 68 1122 1098 1.819 .55 .378 .55 .55 2.205 32 218 .51 .58 70 2240 7440 64 71 60 67 0 916 444 472 .651 801 357 1.535 .447 -.619 -1.16
2 1396 1182 392 355 1004 827 1306 1193 396 367 914 838 0 0 371 393 92 119 100 98 98 94 1831 1752 1.214 .824 .917 .742 .801 2.12 52 232 .828 .81 80 2390 7440 64 72 75 83 0 1400 421 980 .976 1413 993 1.025 1.086 -.035 .119
3 674 493 379 356 295 137 410 406 387 367 31 50 0 0 637 296 87 116 37 35 21 21 432 81 2.153 .464 1.613 .787 .644 3.592 80 394 .362 .57 100 2520 7430 62 72 87 97 -100 584 422 162 .55 481 59 1.818 1.911 -.862 .934
4 1489 882 384 399 1105 483 1558 862 392 407 1174 463 0 0 661 307 102 132 84 78 84 75 1588 1637 2.288 .437 .394 .405 .425 2.77 32 153 .377 .71 60 2690 7440 65 71 106 112 0 1045 473 572 .518 1021 549 1.931 .467 -.949 -1.098
5 2142 1455 372 384 1770 1071 2240 1470 378 399 1868 1086 0 0 567 444 83 129 100 100 100 92 2841 2954 1.653 .605 .581 .569 .583 1.635 52 268 .601 .86 80 2820 7440 64 72 118 126 0 1724 455 1269 .717 1742 1287 1.395 .689 -.48 -.538
6 1849 1436 370 386 1479 1050 1861 1381 377 394 1491 995 0 0 480 367 83 116 100 100 100 100 2529 2486 1.409 .71 .667 .713 .704 1.478 32 210 .655 .86 70 2970 7440 64 71 133 140 0 1701 457 1244 .841 1636 1179 1.189 .791 -.25 -.339
7 1943 1208 377 385 1566 823 2238 1202 378 395 1861 817 0 0 870 503 90 121 94 94 88 84 2389 2678 1.903 .526 .439 .619 .494 3.6 52 261 .431 .71 80 3130 7440 64 72 149 157 0 1431 456 975 .623 1424 968 1.606 .52 -.684 -.943
8 1245 1061 378 387 867 674 1116 985 379 396 738 598 0 0 459 390 92 114 98 96 98 86 1541 1336 1.286 .777 .81 .742 .779 1.968 52 222 .761 .8 80 3260 7440 64 72 162 170 0 1257 458 799 .921 1167 708 1.086 .96 -.119 -.059
9 1381 895 371 377 1010 518 1332 897 382 394 961 520 0 0 361 257 101 136 100 94 100 78 1528 1481 1.95 .513 .541 .5 .536 1.726 52 332 .534 .77 90 3390 7420 61 70 174 183 0 1060 447 614 .608 1063 616 1.646 .641 -.719 -.641
10 1230 783 389 392 841 391 1297 798 397 401 908 406 0 0 261 175 108 134 100 91 100 75 1232 1314 2.151 .465 .447 .409 .481 2.324 12 104 .411 .59 50 3550 7430 64 69 192 197 0 928 464 463 .551 945 481 1.816 .53 -.86 -.917
11 1237 972 372 400 865 572 1172 966 380 411 800 566 0 0 331 296 104 127 100 94 100 82 1437 1366 1.512 .661 .708 .582 .652 1.977 52 330 .699 .78 90 3680 7430 62 71 203 212 0 1152 474 678 .783 1144 671 1.276 .838 -.352 -.255
12 1242 1040 367 397 875 643 1190 930 369 402 823 533 0 0 472 447 90 127 97 90 96 78 1518 1356 1.361 .735 .648 .687 .723 1.92 80 402 .765 .78 100 3840 7430 62 72 219 229 0 1232 470 762 .871 1102 631 1.149 .767 -.2 -.382
13 1623 1219 349 369 1274 850 1553 1145 353 373 1204 776 0 0 518 476 86 120 100 100 100 96 2124 1980 1.499 .667 .645 .618 .645 1.633 52 262 .669 .84 90 3980 7430 62 71 233 242 0 1444 437 1007 .79 1357 919 1.265 .764 -.339 -.389
14 1774 1195 343 350 1431 845 1756 1130 369 366 1413 780 0 0 492 336 153 146 100 100 100 97 2276 2193 1.693 .59 .552 .58 .613 1.438 80 423 .619 .84 110 4110 7430 61 72 245 256 0 1416 415 1001 .7 1339 924 1.429 .654 -.515 -.613
15 1576 1059 353 380 1223 679 1559 1080 383 395 1206 700 0 0 266 268 169 154 100 96 98 91 1902 1906 1.801 .555 .58 .526 .61 1.567 80 321 .563 .83 100 4270 7430 62 72 262 272 0 1255 450 804 .658 1280 829 1.52 .688 -.604 -.54
16 4492 4261 357 368 4135 3893 4706 4401 365 375 4349 4033 0 0 1637 1217 90 113 95 100 95 100 8028 8382 1.062 .941 .927 1.008 .914 1.919 120 457 .898 .93 120 4410 7440 62 74 275 287 0 5048 436 4612 1.115 5214 4778 .897 1.099 .158 .136
17 2381 1931 352 336 2029 1595 2364 1882 374 359 2012 1546 0 0 664 569 149 151 100 100 100 100 3624 3558 1.272 .786 .768 .773 .77 1.449 80 393 .793 .89 110 4550 7430 61 72 289 300 0 2288 398 1890 .931 2230 1832 1.074 .91 -.103 -.136
18 433 426 354 363 79 63 353 389 387 380 -1 26 0 0 274 195 159 160 13 13 8 6 142 25 1.254 .797 null .911 .927 3.313 80 318 .676 .64 100 4710 7430 62 72 306 316 -50 505 430 75 .945 461 31 1.058 null -.082 null
19 4359 3902 365 371 3994 3531 4471 4023 389 400 4106 3652 0 0 1689 1474 141 236 100 100 100 98 7525 7758 1.131 .884 .889 .871 .899 1.387 80 333 .885 .94 110 4840 7430 61 72 318 329 0 4623 440 4183 1.047 4766 4327 .955 1.054 .067 .076
20 2038 1088 355 358 1683 730 2079 1099 378 387 1724 741 0 0 460 271 135 223 100 96 100 85 2413 2465 2.305 .434 .43 .415 .449 1.564 80 381 .446 .77 110 4990 7430 61 72 333 344 0 1289 424 865 .514 1302 878 1.946 .509 -.961 -.974

Total number of rows: 43008

Table truncated, full table size 10004 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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