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Sample GSM84351 Query DataSets for GSM84351
Status Public on Nov 22, 2005
Title TC1 6HR
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 T6 RNA
Organism Helicobacter pylori
Characteristics T6 RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14840.gif
Measurement: time(absolute) 6 h
name: 14840_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 3766 4269 364 275 3402 3994 3902 4608 370 286 3538 4333 0 0 1020 1208 93 81 100 100 100 100 7396 7871 .852 1.174 1.225 1.169 1.178 1.161 120 868 1.192 .98 130 1670 40990 52 65 32 45 0 3933 253 3680 1.082 4245 3992 .925 1.128 .113 .174
2 831 744 351 255 480 489 789 685 361 266 438 430 0 0 231 266 89 76 98 98 96 95 969 868 .982 1.019 .982 .981 1.004 1.63 156 1080 1.028 .88 150 1920 40990 51 66 56 71 0 685 235 451 .939 631 396 1.065 .904 -.091 -.145
3 1510 1979 333 243 1177 1736 1463 1909 338 244 1130 1666 0 0 430 632 67 53 100 100 99 100 2913 2796 .678 1.475 1.474 1.489 1.483 1.397 208 1294 1.501 .95 160 2170 40990 51 67 81 97 0 1823 224 1599 1.359 1759 1535 .736 1.358 .442 .442
4 861 817 314 236 547 581 817 839 317 237 503 603 0 0 253 242 59 53 100 100 100 100 1128 1106 .941 1.062 1.199 1.09 1.07 1.472 52 340 1.036 .9 80 2410 40980 54 62 109 117 0 753 217 535 .979 773 556 1.022 1.104 -.031 .143
5 890 819 315 226 575 593 803 737 316 231 488 511 0 0 354 372 64 53 97 98 92 96 1168 999 .97 1.031 1.047 1.053 .987 1.782 80 560 1.04 .92 100 2640 40980 53 63 131 141 0 755 208 546 .95 679 471 1.052 .965 -.074 -.052
6 903 831 323 234 580 597 859 765 328 239 536 531 0 0 260 309 69 55 100 99 98 97 1177 1067 .972 1.029 .991 .979 1.023 1.523 208 1368 1.064 .9 170 2890 40980 49 66 152 169 0 766 216 550 .948 705 489 1.055 .913 -.077 -.132
7 1278 1106 330 239 948 867 1138 966 332 246 808 727 0 0 681 612 73 60 100 100 96 95 1815 1535 1.093 .915 .9 .892 .908 1.534 80 554 .897 .94 100 3130 40980 53 63 180 190 0 1019 220 799 .843 890 670 1.187 .829 -.247 -.271
8 2126 967 317 236 1809 731 1071 540 323 241 754 304 0 0 2003 863 69 57 100 93 97 82 2540 1058 2.475 .404 .403 .365 .385 1.627 208 1190 .388 .88 160 3380 40980 50 66 202 218 0 891 217 673 .372 497 280 2.686 .371 -1.426 -1.429
9 3421 1576 316 239 3105 1337 3111 1464 321 241 2795 1225 0 0 1721 699 69 57 100 100 100 100 4442 4020 2.322 .431 .438 .45 .431 1.47 256 1367 .408 .97 180 3610 40980 49 67 224 242 0 1452 220 1232 .397 1349 1129 2.521 .404 -1.334 -1.308
10 1031 1017 314 244 717 773 873 849 317 243 559 605 0 0 447 421 63 58 98 98 97 98 1490 1164 .928 1.078 1.082 1.102 1.158 1.474 80 528 1.056 .94 100 3850 40980 53 63 252 262 0 937 225 712 .993 782 557 1.007 .997 -.01 -.004
11 1191 932 305 242 886 690 1029 816 310 244 724 574 0 0 497 337 81 57 100 100 100 100 1576 1298 1.284 .779 .793 .804 .818 1.372 120 876 .738 .92 130 4080 40980 51 64 273 286 0 859 223 636 .717 752 529 1.394 .73 -.479 -.453
12 976 948 308 235 668 713 972 953 313 242 664 718 0 0 183 200 75 69 100 100 100 99 1381 1382 .937 1.067 1.081 1.061 1.062 1.286 208 1223 1.068 .94 160 4330 40980 50 66 297 313 0 873 217 657 .983 878 661 1.017 .996 -.024 -.005
13 1537 1462 303 233 1234 1229 1487 1443 310 239 1184 1210 0 0 463 448 75 76 100 100 99 98 2463 2394 1.004 .996 1.022 .994 1.002 1.294 156 1004 .968 .95 150 4560 40970 49 64 320 335 0 1347 215 1132 .918 1329 1115 1.09 .942 -.124 -.087
14 2032 2342 295 225 1737 2117 2031 2433 302 231 1736 2208 0 0 554 749 73 68 100 100 100 100 3854 3944 .821 1.219 1.272 1.188 1.212 1.295 208 1304 1.247 .97 170 4800 40970 48 65 343 360 0 2158 207 1950 1.123 2242 2034 .891 1.172 .167 .229
15 1365 752 292 230 1073 522 1495 776 303 238 1203 546 0 0 305 168 87 79 100 100 98 94 1595 1749 2.056 .486 .454 .483 .483 1.379 52 412 .474 .92 90 5040 40960 51 60 371 380 0 693 212 481 .448 715 503 2.231 .418 -1.158 -1.258
16 807 1056 281 217 526 839 769 924 283 218 488 707 0 0 419 463 65 54 96 100 84 100 1365 1195 .627 1.595 1.449 1.967 1.77 1.786 32 176 1.413 .91 60 5280 40980 55 61 397 403 0 973 200 773 1.47 851 651 .68 1.335 .555 .417
17 1190 2173 268 203 922 1970 883 1614 275 203 615 1411 0 0 761 1473 70 48 100 100 96 100 2892 2026 .468 2.137 2.294 2.284 2.039 1.421 52 420 2.087 .96 90 5520 40980 53 62 419 428 0 2002 187 1815 1.968 1487 1300 .508 2.114 .977 1.08
18 1529 1037 362 264 1167 773 1573 1014 366 268 1211 750 0 0 388 246 68 64 100 100 100 100 1940 1961 1.51 .662 .619 .67 .676 1.363 32 220 .615 .93 70 1680 41230 79 86 36 43 0 955 243 712 .61 934 691 1.639 .571 -.713 -.81
19 1212 1000 331 231 881 769 1176 1019 335 239 845 788 0 0 347 312 69 58 100 99 99 97 1650 1633 1.146 .873 .933 .852 .866 1.497 120 826 .873 .93 130 1920 41240 77 90 57 70 0 921 213 708 .804 939 726 1.244 .859 -.314 -.219
20 1082 933 315 220 767 713 1172 993 318 222 857 773 0 0 380 333 66 52 100 94 98 94 1480 1630 1.076 .93 .902 .889 .93 2.208 52 332 .895 .93 80 2170 41230 79 87 85 93 0 860 203 657 .856 915 712 1.168 .831 -.224 -.267

Total number of rows: 4608

Table truncated, full table size 1059 Kbytes.




Supplementary data files not provided
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