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Sample GSM88813 Query DataSets for GSM88813
Status Public on Dec 22, 2005
Title Stat Chelate T=90m
Sample type RNA
 
Channel 1
Source name 1ug Stat Chelate T=0
Organism Helicobacter pylori
Characteristics 1ug Stat Chelate T=0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1ug Stat chelate T=90min
Organism Helicobacter pylori
Characteristics 1ug Stat chelate T=90min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31385.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 Dec 21, 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)
GSE3888 Growth phase-dependent response of Helicobacter pylori to iron starvation.

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 3028 2369 195 188 2833 2181 3078 2402 210 208 2883 2214 0 0 605 433 179 237 100 100 100 100 5014 5097 1.299 .77 .768 .774 .771 1.122 52 346 .76 .98 90 1870 39380 49 58 62 71 0 2662 211 2451 .865 2699 2488 1.156 .863 -.209 -.213
2 974 738 201 196 773 542 909 743 204 197 708 547 0 0 327 201 35 54 100 100 100 98 1315 1255 1.426 .701 .773 .719 .713 1.429 52 420 .671 .92 90 2120 39390 50 59 87 96 0 829 220 609 .788 835 615 1.269 .868 -.344 -.204
3 1275 858 180 181 1095 677 1117 722 182 190 937 541 0 0 680 426 27 112 100 96 100 84 1772 1478 1.617 .618 .577 .612 .616 1.498 52 420 .628 .9 90 2370 39390 50 59 112 121 0 964 203 761 .695 811 608 1.44 .649 -.526 -.624
4 389 285 178 185 211 100 310 271 179 187 132 86 0 0 171 107 26 48 90 68 78 46 311 218 2.11 .474 .652 .564 .637 1.956 32 176 .516 .66 60 2610 39390 52 58 138 144 0 320 208 112 .533 304 97 1.878 .732 -.909 -.45
5 504 279 178 187 326 92 507 270 178 191 329 83 0 0 82 90 26 54 100 66 100 41 418 412 3.543 .282 .252 .242 .266 2.35 12 104 .319 .46 50 2860 39400 53 58 163 168 0 313 210 103 .317 303 93 3.154 .283 -1.657 -1.819
6 619 570 192 198 427 372 591 569 195 200 399 371 0 0 191 186 34 49 100 100 100 100 799 770 1.148 .871 .93 .848 .891 1.565 32 236 .876 .86 70 3080 39390 51 58 184 191 0 640 222 418 .979 639 417 1.022 1.045 -.031 .063
7 1021 746 190 201 831 545 963 702 191 206 773 501 0 0 448 289 28 75 100 100 100 98 1376 1274 1.525 .656 .648 .683 .62 1.639 52 420 .632 .9 90 3340 39380 49 58 209 218 0 838 226 612 .737 789 563 1.357 .728 -.44 -.458
8 1229 927 192 194 1037 733 1166 900 195 202 974 706 0 0 490 333 30 52 100 98 100 98 1770 1680 1.415 .707 .725 .682 .711 1.455 52 420 .692 .94 90 3570 39380 49 58 232 241 0 1042 218 824 .794 1011 793 1.259 .814 -.332 -.296
9 2954 1550 203 201 2751 1349 3296 1661 205 207 3093 1460 0 0 1130 535 35 57 100 100 100 100 4100 4553 2.039 .49 .472 .497 .505 1.246 52 420 .479 .97 90 3810 39380 49 58 256 265 0 1742 226 1516 .551 1866 1640 1.815 .53 -.86 -.915
10 791 698 210 213 581 485 776 682 210 218 566 469 0 0 239 197 30 61 100 100 100 100 1066 1035 1.198 .835 .829 .831 .868 1.421 32 236 .828 .91 70 4060 39380 50 57 282 289 0 784 239 545 .938 766 527 1.066 .931 -.092 -.103
11 737 618 240 251 497 367 741 632 244 257 501 381 0 0 160 102 41 67 100 100 100 100 864 882 1.354 .738 .76 .745 .715 1.24 12 104 .713 .9 50 4290 39390 52 57 306 311 0 694 282 412 .83 710 428 1.205 .854 -.269 -.227
12 1146 1036 237 228 909 808 1163 1013 241 232 926 785 0 0 237 201 47 64 100 100 100 100 1717 1711 1.125 .889 .848 .897 .909 1.233 52 420 .878 .94 90 4530 39380 49 58 328 337 0 1164 256 908 .999 1138 882 1.001 .953 -.002 -.07
13 1172 1124 245 234 927 890 1066 1025 251 241 821 791 0 0 439 425 42 68 100 100 100 100 1817 1612 1.042 .96 .963 .952 .979 1.318 52 420 .966 .95 90 4780 39390 50 59 353 362 0 1263 263 1000 1.079 1152 889 .927 1.083 .109 .114
14 2110 1681 269 251 1841 1430 2111 1678 278 258 1842 1427 0 0 572 460 70 73 100 100 100 100 3271 3269 1.287 .777 .775 .771 .814 1.276 32 236 .757 .95 70 5010 39390 51 58 377 384 0 1889 282 1607 .873 1885 1603 1.146 .87 -.196 -.2
15 982 631 258 252 724 379 1014 626 258 253 756 374 0 0 385 311 41 63 100 87 100 81 1103 1130 1.91 .523 .495 .462 .486 1.89 32 176 .6 .89 60 5260 39390 52 58 403 409 0 709 283 426 .588 703 420 1.7 .556 -.766 -.847
16 1050 1546 253 250 797 1296 1096 1649 256 252 843 1399 0 0 378 584 37 70 100 100 100 100 2093 2242 .615 1.626 1.66 1.635 1.6 1.344 32 236 1.627 .95 70 5490 39390 51 58 425 432 0 1737 281 1456 1.827 1853 1572 .547 1.865 .87 .899
17 1521 1472 243 242 1278 1230 1508 1437 255 255 1265 1195 0 0 715 646 90 94 100 100 100 100 2508 2460 1.039 .962 .945 1 .984 1.298 32 236 .943 .97 70 5720 39380 50 57 448 455 0 1654 272 1382 1.081 1615 1343 .925 1.061 .113 .086
18 1095 1205 185 179 910 1026 1023 1095 214 214 838 916 0 0 598 717 274 285 82 82 63 63 1936 1754 .887 1.127 1.093 1.099 1.094 1.718 52 320 1.155 .97 80 1900 39620 74 82 66 74 0 1354 201 1153 1.267 1230 1029 .789 1.228 .341 .297
19 1058 779 202 191 856 588 935 779 204 196 733 588 0 0 415 310 36 56 100 100 100 96 1444 1321 1.456 .687 .802 .655 .686 1.494 32 236 .725 .92 70 2160 39630 75 82 92 99 0 875 215 661 .772 875 661 1.296 .901 -.374 -.15
20 594 427 180 190 414 237 534 345 182 185 354 155 0 0 248 166 31 49 100 91 100 91 651 509 1.747 .572 .438 .525 .602 1.529 12 104 .652 .89 50 2400 39630 76 81 117 122 0 480 213 266 .643 388 174 1.555 .492 -.637 -1.023

Total number of rows: 4608

Table truncated, full table size 1044 Kbytes.




Supplementary data files not provided
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