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Sample GSM741266 Query DataSets for GSM741266
Status Public on Nov 02, 2012
Title shfc108|HCT116
Sample type genomic
 
Channel 1
Source name Normal human male genomic DNA
Organism Homo sapiens
Characteristics reference: Normal human male genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name HCT116 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: HCT116
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol model: GenePix 4000B
Description Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68860.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 Jun 14, 2011
Last update date Nov 02, 2012
Contact name Keyan Salari
E-mail(s) [email protected]
Organization name Massachusetts General Hospital
Street address Gray/Bigelow Rm 1102, 55 Fruit Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL9073
Series (2)
GSE29953 Colorectal Cancer Cell Lines aCGH
GSE30475 Colorectal Cancer Cells

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 1319 1370 219 312 1100 1058 1356 1283 229 391 1137 971 0 0 407 654 102 314 98 94 96 71 2158 2108 1.04 .962 .854 1.51 .87 2.62 80 293 1.02 .95 100 2510 5400 67 77 58 68 0 1308 298 1010 .918 1225 927 1.089 .815 -.123 -.294
2 1568 956 220 337 1348 619 1592 960 233 402 1372 623 0 0 389 459 102 308 100 72 100 52 1967 1995 2.178 .459 .454 .5 .42 .39 64 286 .61 .95 90 2650 5390 66 75 72 81 0 913 322 591 .438 917 595 2.281 .434 -1.19 -1.206
3 2186 1893 250 381 1936 1512 2051 1951 265 447 1801 1570 0 0 563 770 109 335 100 92 100 80 3448 3371 1.28 .781 .872 .84 .87 .44 60 337 .88 .98 80 2790 5390 67 75 87 95 0 1807 364 1444 .746 1863 1499 1.341 .832 -.423 -.265
4 1047 1548 263 406 784 1142 1120 1436 283 455 857 1030 0 0 286 870 125 318 98 88 98 73 1926 1887 .687 1.457 1.202 1.63 1.45 1.19 52 356 1.5 .92 80 2950 5390 67 75 103 111 0 1478 388 1090 1.391 1371 983 .719 1.148 .476 .199
5 767 1142 252 430 515 712 747 1040 266 515 495 610 0 0 206 587 122 364 97 81 94 39 1227 1105 .723 1.383 1.232 1.69 1.27 1.33 36 345 1.51 .95 70 3090 5390 67 74 117 124 0 1090 411 680 1.32 993 582 .758 1.177 .401 .235
6 2227 3642 244 511 1983 3131 2207 3380 254 573 1963 2869 0 0 498 1025 99 368 100 100 100 100 5114 4832 .633 1.579 1.462 1.62 1.64 .52 52 373 1.65 .99 80 3230 5390 67 75 131 139 0 3477 488 2989 1.508 3227 2739 .663 1.395 .592 .481
7 819 1549 256 517 563 1032 821 1456 266 589 565 939 0 0 244 631 111 395 100 85 88 62 1595 1504 .546 1.833 1.662 2.53 1.79 2.03 34 381 1.87 .95 60 3380 5390 68 74 147 153 0 1479 494 985 1.75 1390 897 .571 1.587 .807 .666
8 1543 1939 259 526 1284 1413 1525 1665 273 581 1266 1139 0 0 401 952 115 372 100 91 98 73 2697 2405 .909 1.1 .9 1.25 .93 1 44 330 1.26 .94 70 3520 5390 67 74 160 167 0 1851 502 1349 1.051 1590 1087 .952 .859 .071 -.219
9 906 1242 252 481 654 761 981 1176 263 566 729 695 0 0 390 666 111 374 88 69 76 46 1415 1424 .859 1.164 .953 1.72 1.32 1.95 102 275 1.4 .95 110 3670 5370 63 74 173 184 0 1186 459 727 1.111 1123 664 .9 .91 .152 -.136
10 1990 2438 256 483 1734 1955 2006 2513 263 554 1750 2030 0 0 446 1033 101 368 100 95 100 87 3689 3780 .887 1.127 1.16 1.19 1.15 .65 104 209 1.23 .97 110 3810 5390 65 76 187 198 0 2328 461 1867 1.076 2399 1938 .929 1.108 .106 .147
11 868 1112 266 457 602 655 858 1024 281 527 592 567 0 0 223 543 110 353 100 63 99 44 1257 1159 .919 1.088 .958 1.37 1.02 1.11 80 231 1.31 .93 100 3960 5390 66 76 203 213 0 1062 436 625 1.039 978 541 .963 .914 .055 -.129
12 1158 1330 267 486 891 844 1126 1254 285 555 859 768 0 0 322 630 112 358 99 72 99 53 1735 1627 1.056 .947 .894 1.13 .96 .89 97 285 1.18 .94 110 4100 5380 64 75 216 227 0 1270 464 806 .904 1197 733 1.106 .854 -.145 -.228
13 1484 1918 264 480 1220 1438 1469 1848 278 555 1205 1368 0 0 315 766 110 394 100 95 100 80 2658 2573 .848 1.179 1.135 1.27 1.04 .72 80 254 1.29 .97 100 4250 5390 66 76 232 242 0 1831 458 1373 1.125 1764 1306 .889 1.084 .17 .116
14 1591 1955 258 500 1333 1455 1584 1899 274 574 1326 1399 0 0 362 790 111 393 100 93 100 83 2788 2725 .916 1.092 1.055 1.17 1.03 .71 112 221 1.24 .95 120 4400 5390 65 77 246 258 0 1867 477 1389 1.042 1813 1336 .96 1.007 .06 .011
15 812 1101 293 455 519 646 837 979 301 550 544 524 0 0 186 530 124 414 99 62 93 26 1165 1068 .803 1.245 .963 1.62 1.25 1.38 86 256 1.33 .92 100 4540 5380 65 75 261 271 0 1051 434 617 1.188 935 500 .841 .92 .249 -.121
16 5649 7467 306 485 5343 6982 5624 7350 314 547 5318 6865 0 0 1064 1710 124 393 100 100 100 100 12325 12183 .765 1.307 1.291 1.36 1.28 .48 80 280 1.32 .99 100 4690 5390 66 76 276 286 0 7129 463 6666 1.248 7018 6555 .802 1.233 .319 .302
17 1792 2506 317 533 1475 1973 1855 2370 334 596 1538 1837 0 0 351 858 165 379 100 99 100 97 3448 3375 .748 1.338 1.194 1.43 1.33 .71 86 267 1.41 .97 100 4840 5380 65 75 291 301 0 2393 509 1884 1.277 2263 1754 .783 1.14 .353 .19
18 1797 2319 293 435 1504 1884 1786 2197 316 481 1493 1762 0 0 369 832 172 300 100 99 100 96 3388 3255 .798 1.253 1.18 1.31 1.15 .69 97 249 1.32 .97 110 4980 5380 64 75 304 315 0 2214 415 1799 1.196 2098 1682 .836 1.127 .258 .172
19 4599 5459 275 398 4324 5061 4495 5332 286 457 4220 4934 0 0 1242 1504 112 311 100 100 100 100 9385 9154 .854 1.17 1.169 1.2 1.15 .36 104 238 1.19 .98 110 5130 5380 64 75 319 330 0 5212 380 4832 1.118 5091 4711 .895 1.116 .16 .159
20 1311 1451 258 361 1053 1090 1269 1363 263 429 1011 1002 0 0 261 650 105 308 100 91 100 72 2143 2013 .966 1.035 .991 1.14 1.02 .74 97 258 1.11 .95 110 5270 5380 64 75 333 344 0 1385 345 1041 .988 1301 957 1.012 .946 -.017 -.08

Total number of rows: 41472

Table truncated, full table size 9569 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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