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Sample GSM84360 Query DataSets for GSM84360
Status Public on Nov 22, 2005
Title TC1 48HR
Sample type RNA
 
Channel 1
Source name Original SS1 RNA
Organism Helicobacter pylori
Characteristics Original SS1 RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name T48 RNA
Organism Helicobacter pylori
Characteristics T48 RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14849.gif
Measurement: time(absolute) 48 h
name: 14849_Elapsed Time
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 18, 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 GPL15
Series (1)
GSE3636 Growth phase dependent gene expression and motility_3 time courses

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 1581 1117 384 226 1197 891 1556 1077 387 231 1172 851 0 0 549 403 81 60 100 98 96 97 2088 2023 1.343 .744 .726 .75 .755 1.88 80 538 .717 .91 100 1640 13520 63 73 43 53 0 740 150 590 .493 764 604 2.029 .515 -1.02 -.957
2 608 502 400 245 208 257 580 514 1625 681 180 269 0 0 202 213 5909 2068 0 0 0 0 465 449 .809 1.236 1.494 1.312 1.113 2.987 52 332 .286 .97 80 1860 13490 61 69 66 74 0 332 162 170 .818 365 191 1.222 1.06 -.289 .084
3 932 724 407 236 525 488 900 705 422 247 493 469 0 0 280 224 114 93 93 98 81 93 1013 962 1.076 .93 .951 .954 .886 1.887 80 560 .888 .81 100 2120 13510 62 72 91 101 0 479 156 323 .616 500 333 1.624 .675 -.7 -.568
4 694 615 414 227 280 388 662 528 419 238 248 301 0 0 210 303 90 63 81 87 59 78 668 549 .722 1.386 1.214 1.163 1.433 2.51 32 176 1.454 .74 60 2360 13500 63 69 117 123 0 407 150 257 .918 374 213 1.09 .861 -.124 -.216
5 1038 929 394 231 644 698 989 1029 402 234 595 798 0 0 267 315 81 53 100 100 100 100 1342 1393 .923 1.084 1.341 1.022 1.235 1.836 12 68 1.151 .85 40 2600 13500 64 68 142 146 0 615 153 462 .718 730 566 1.393 .951 -.478 -.072
6 860 756 369 221 491 535 832 746 375 226 463 525 0 0 242 203 83 60 98 100 94 100 1026 988 .918 1.09 1.134 1.177 1.158 1.762 156 1224 1.045 .82 150 2840 13510 59 74 160 175 0 501 146 354 .722 529 372 1.386 .804 -.471 -.314
7 790 817 376 221 414 596 797 739 377 226 421 518 0 0 185 262 78 64 96 100 93 100 1010 939 .695 1.44 1.23 1.491 1.426 1.475 32 236 1.421 .84 70 3090 13500 62 69 189 196 0 541 146 395 .953 524 367 1.049 .873 -.069 -.197
8 967 1068 368 223 599 845 783 1010 368 233 415 787 0 0 462 666 83 65 87 87 84 84 1444 1202 .709 1.411 1.896 1.245 1.292 2.951 32 160 1.462 .87 60 3320 13480 61 67 213 219 0 707 148 560 .934 716 558 1.07 1.345 -.098 .428
9 2636 1287 406 234 2230 1053 2746 1443 433 261 2340 1209 0 0 1206 657 182 107 96 93 93 87 3283 3549 2.118 .472 .517 .411 .484 2.17 32 223 .48 .94 70 3540 13480 60 67 234 241 0 852 155 697 .313 1023 857 3.198 .366 -1.677 -1.448
10 811 902 428 249 383 653 725 764 428 255 297 515 0 0 354 425 84 61 84 100 68 96 1036 812 .587 1.705 1.734 2.002 1.815 2.296 32 176 1.496 .76 60 3800 13500 63 69 261 267 0 597 165 432 1.129 542 365 .886 1.23 .175 .298
11 1352 1236 420 279 932 957 1420 1217 425 288 1000 938 0 0 215 329 97 70 100 100 100 100 1889 1938 .974 1.027 .938 .997 1.018 1.231 12 98 1.099 .92 50 4010 13480 61 66 282 287 0 819 185 634 .68 863 665 1.471 .665 -.556 -.588
12 949 1120 398 249 551 871 966 1106 399 255 568 857 0 0 188 235 84 68 99 100 99 100 1422 1425 .633 1.581 1.509 1.631 1.645 1.402 120 814 1.621 .89 120 4260 13500 60 72 304 316 0 742 165 577 1.047 784 608 .955 1.07 .066 .098
13 1238 1635 403 250 835 1385 1194 1660 410 254 791 1410 0 0 338 437 92 76 99 100 98 98 2220 2201 .603 1.659 1.783 1.696 1.717 1.539 120 913 1.661 .91 130 4510 13490 58 71 328 341 0 1083 166 917 1.098 1177 1000 .91 1.264 .135 .338
14 1622 1526 414 254 1208 1272 1705 1488 429 269 1291 1234 0 0 592 512 136 110 100 100 96 100 2480 2525 .95 1.053 .956 1.123 1.108 1.638 32 236 .993 .89 70 4730 13490 61 68 353 360 0 1011 168 842 .697 1055 875 1.434 .678 -.52 -.561
15 2252 779 407 246 1845 533 2310 819 414 252 1903 573 0 0 332 167 99 63 100 100 100 91 2378 2476 3.462 .289 .301 .271 .276 1.546 12 90 .287 .89 50 4990 13470 60 65 380 385 0 516 163 353 .191 581 406 5.227 .214 -2.386 -2.227
16 832 572 393 247 439 325 815 537 401 250 422 290 0 0 201 190 85 63 100 96 90 87 764 712 1.351 .74 .687 .684 .801 2.037 32 236 .708 .73 70 5230 13490 61 68 403 410 0 379 164 215 .49 381 206 2.04 .487 -1.028 -1.037
17 1192 486 414 242 778 244 1046 455 418 249 632 213 0 0 458 183 86 70 100 80 100 67 1022 845 3.189 .314 .337 .252 .271 2.354 52 420 .295 .74 90 5470 13490 60 69 426 435 0 322 160 162 .208 323 151 4.815 .239 -2.267 -2.065
18 2254 988 394 233 1860 755 2259 1115 397 234 1865 882 0 0 502 380 91 56 100 100 100 100 2615 2747 2.464 .406 .473 .361 .38 1.831 12 62 .398 .81 40 1650 13730 87 91 47 51 0 654 154 500 .269 791 626 3.72 .335 -1.895 -1.576
19 831 914 377 239 454 675 808 871 382 246 431 632 0 0 121 318 98 69 100 100 100 100 1129 1063 .673 1.487 1.466 1.374 1.464 1.715 12 104 2.061 .69 50 1880 13740 87 92 69 74 0 605 158 447 .985 618 448 1.016 1.04 -.022 .057
20 784 612 388 227 396 385 783 609 373 229 395 382 0 0 276 158 72 60 91 100 75 100 781 777 1.029 .972 .967 1.046 1.288 1.814 12 68 .741 .66 40 2130 13740 88 92 95 99 0 405 150 255 .644 432 271 1.553 .686 -.635 -.544

Total number of rows: 4608

Table truncated, full table size 1041 Kbytes.




Supplementary data files not provided
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