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Sample GSM88823 Query DataSets for GSM88823
Status Public on Dec 22, 2005
Title Log.iron.survival.30
Sample type RNA
 
Channel 1
Source name 1 ug of Hp RNA from T=0 log culture
Organism Helicobacter pylori
Characteristics 1 ug of Hp RNA from T=0 log culture
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1ug of Hp RNA from T=30 log culture
Organism Helicobacter pylori
Characteristics 1ug of Hp RNA from T=30 log culture
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32056.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 3567 3015 103 103 3464 2912 3387 2912 107 109 3284 2809 0 0 1512 1121 27 34 100 100 100 100 6376 6093 1.19 .841 .855 .863 .868 1.146 52 312 .821 .94 80 1190 40740 42 50 55 63 0 2233 76 2157 .623 2157 2081 1.606 .634 -.683 -.658
2 836 923 109 106 727 817 734 782 123 139 625 676 0 0 453 442 56 144 100 100 98 96 1544 1301 .89 1.124 1.082 1.208 1.191 1.354 52 420 1.141 .93 90 1410 40750 42 51 76 85 0 684 79 605 .832 579 501 1.201 .801 -.265 -.32
3 1783 1822 112 113 1671 1709 900 1012 117 118 788 899 0 0 1540 1771 27 35 100 98 100 98 3380 1687 .978 1.023 1.141 .973 .92 1.538 52 320 1.097 .94 80 1670 40740 42 50 103 111 0 1350 84 1266 .758 750 666 1.32 .845 -.401 -.243
4 970 2075 119 128 851 1947 1085 1566 126 132 966 1438 0 0 450 1659 39 33 100 100 91 100 2798 2404 .437 2.288 1.489 2.291 1.99 2.255 12 104 2.517 .87 50 1900 40760 45 50 127 132 0 1537 95 1442 1.695 1160 1065 .59 1.103 .761 .141
5 1141 1822 156 167 985 1655 584 1151 166 182 428 984 0 0 1317 2141 68 72 75 81 65 81 2640 1412 .595 1.68 2.299 2.294 1.902 2.774 32 176 1.815 .8 60 2150 40760 45 51 152 158 0 1350 124 1226 1.245 853 729 .803 1.703 .316 .768
6 706 1282 181 209 525 1073 462 645 314 390 281 436 0 0 778 1921 577 752 23 26 11 15 1598 717 .489 2.044 1.552 1.662 1.624 2.321 52 340 2.745 .82 80 2380 40760 44 52 174 182 0 950 155 795 1.514 478 323 .661 1.149 .598 .201
7 1506 2438 115 121 1391 2317 1464 2289 116 125 1349 2168 0 0 1188 1664 28 31 100 100 100 100 3708 3517 .6 1.666 1.607 1.879 1.492 1.767 32 170 1.577 .94 60 2640 40740 43 49 201 207 0 1806 90 1716 1.234 1696 1606 .81 1.19 .303 .252
8 1370 2255 109 119 1261 2136 1393 2092 112 125 1284 1973 0 0 749 1551 25 33 100 100 100 100 3397 3257 .59 1.694 1.537 1.756 1.739 1.371 52 320 1.732 .84 80 2860 40730 41 49 222 230 0 1670 88 1582 1.255 1550 1461 .797 1.138 .327 .187
9 2870 3217 114 125 2756 3092 2458 3044 131 151 2344 2919 0 0 2205 2371 65 103 96 90 91 85 5848 5263 .891 1.122 1.245 1.066 1.116 1.852 80 538 1.104 .96 100 3110 40730 40 50 246 256 0 2383 93 2290 .831 2255 2162 1.203 .922 -.267 -.116
10 1110 2310 108 115 1002 2195 497 1180 112 121 389 1065 0 0 1359 2886 34 34 100 100 96 96 3197 1454 .456 2.191 2.738 2.052 2.173 1.767 32 230 2.105 .94 70 3360 40730 41 48 272 279 0 1711 85 1626 1.623 874 789 .616 2.028 .698 1.02
11 912 1739 113 118 799 1621 504 1190 114 123 391 1072 0 0 902 1906 27 31 100 100 100 100 2420 1463 .493 2.029 2.742 2.116 2.129 1.837 32 236 2.025 .91 70 3590 40740 42 49 295 302 0 1288 87 1201 1.503 881 794 .665 2.031 .588 1.022
12 1400 2069 111 119 1289 1950 1374 2094 115 125 1263 1975 0 0 468 614 35 30 100 100 100 100 3239 3238 .661 1.513 1.564 1.537 1.446 1.398 52 300 1.616 .91 80 3820 40710 39 47 318 326 0 1533 88 1444 1.121 1551 1463 .892 1.158 .164 .212
13 1118 2007 115 128 1003 1879 613 1067 124 139 498 939 0 0 1033 2202 41 55 100 100 100 100 2882 1437 .534 1.873 1.886 1.692 1.71 1.44 52 420 1.999 .88 90 4060 40730 40 49 341 350 0 1487 95 1392 1.388 790 696 .721 1.397 .473 .482
14 2404 3271 144 166 2260 3105 1897 2654 147 173 1753 2488 0 0 2079 2876 36 46 100 100 100 100 5365 4241 .728 1.374 1.419 1.337 1.314 1.496 52 400 1.423 .95 90 4300 40710 38 47 365 374 0 2423 123 2300 1.018 1966 1843 .983 1.051 .025 .072
15 1032 1502 146 164 886 1338 682 1040 158 176 536 876 0 0 812 1223 58 54 98 100 90 98 2224 1412 .662 1.51 1.634 1.572 1.424 1.825 52 332 1.865 .9 80 4530 40730 41 49 389 397 0 1113 121 991 1.119 770 649 .894 1.211 .162 .276
16 1174 2305 147 169 1027 2136 493 818 230 290 346 649 0 0 1187 2484 452 713 43 46 34 43 3163 995 .481 2.08 1.876 2.018 1.947 1.515 32 220 2.032 .9 70 4770 40710 39 46 413 420 0 1707 125 1582 1.541 606 481 .649 1.389 .624 .474
17 1435 1637 149 174 1286 1463 588 524 170 204 439 350 0 0 1912 2492 90 121 80 83 73 58 2749 789 .879 1.138 .797 1.018 1.012 1.965 80 656 1.3 .89 110 5020 40730 39 50 436 447 0 1213 129 1084 .843 388 259 1.187 .591 -.247 -.76
18 956 1632 104 108 852 1524 677 1347 109 112 573 1239 0 0 793 1431 37 31 92 98 86 96 2376 1812 .559 1.789 2.162 1.75 1.778 1.789 52 400 1.672 .89 90 1170 40980 65 74 52 61 0 1209 80 1129 1.325 998 918 .755 1.602 .406 .68
19 937 1218 105 106 832 1112 450 575 112 118 345 469 0 0 1150 1450 38 50 90 88 82 84 1944 814 .748 1.337 1.359 1.352 1.289 2.603 52 340 1.46 .64 80 1420 40990 67 75 78 86 0 902 79 824 .99 426 347 1.01 1.007 -.014 .01
20 1032 1942 104 102 928 1840 994 2027 107 111 890 1925 0 0 624 809 24 33 100 100 100 100 2768 2815 .504 1.983 2.163 2.389 2.11 2.362 12 68 1.765 .8 40 1670 41010 71 75 105 109 0 1439 76 1363 1.469 1501 1426 .681 1.602 .555 .68

Total number of rows: 4608

Table truncated, full table size 1057 Kbytes.




Supplementary data files not provided
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