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Sample GSM88793 Query DataSets for GSM88793
Status Public on Dec 22, 2005
Title Stat.iron.survival.0
Sample type RNA
 
Channel 1
Source name 1 ug of Hp RNA from T=0 stationary culture
Organism Helicobacter pylori
Characteristics 1 ug of Hp RNA from T=0 stationary culture
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1 ug of Hp RNA from T=0 stationary culture
Organism Helicobacter pylori
Characteristics 1 ug of Hp RNA from T=0 stationary culture
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32058.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 1298 1127 82 52 1216 1075 1142 981 568 102 1060 929 0 0 492 472 5279 543 0 98 0 38 2291 1989 1.131 .884 .876 .882 .877 1.33 52 320 .106 .82 80 1150 41100 46 54 43 51 0 916 42 874 .719 798 755 1.391 .713 -.476 -.489
2 476 356 70 49 406 307 324 272 71 50 254 223 0 0 291 197 16 12 100 100 96 100 713 477 1.322 .756 .878 .879 .827 1.764 52 340 .776 .9 80 1400 41100 46 54 68 76 0 289 40 250 .615 221 181 1.627 .714 -.702 -.486
3 424 397 67 48 357 349 243 233 69 49 176 185 0 0 323 331 14 10 96 96 94 96 706 361 1.023 .978 1.051 .895 .878 2.193 52 332 1.004 .91 80 1640 41090 45 53 92 100 0 323 39 284 .795 189 150 1.258 .855 -.331 -.227
4 215 193 68 49 147 144 131 115 69 50 63 66 0 0 164 252 14 10 81 84 78 78 291 129 1.021 .98 1.048 .704 .607 3.34 32 176 1.649 .6 60 1870 41100 47 53 116 122 0 157 40 117 .796 93 54 1.256 .852 -.328 -.232
5 430 309 69 46 361 263 388 239 70 48 319 193 0 0 242 252 14 10 100 100 100 100 624 512 1.373 .729 .605 .663 .671 2.235 12 68 .773 .81 40 2120 41110 49 53 142 146 0 251 37 214 .592 194 157 1.688 .492 -.756 -1.024
6 105 108 68 50 37 58 83 65 82 62 15 15 0 0 89 177 72 62 12 12 5 5 95 30 .638 1.568 1 1.14 1.333 3.85 80 649 1.177 .79 110 2350 41090 43 54 161 172 -50 88 41 47 1.274 53 12 .785 .813 .35 -.299
7 402 373 66 49 336 324 275 365 67 51 209 316 0 0 276 239 14 12 100 100 100 100 660 525 1.037 .964 1.512 1.065 1.01 1.607 32 236 .909 .92 70 2590 41090 45 52 187 194 0 303 40 263 .784 297 257 1.276 1.229 -.351 .298
8 819 963 64 51 755 912 589 839 73 63 525 788 0 0 601 661 78 129 90 100 81 81 1667 1313 .828 1.208 1.501 1.378 1.262 1.405 32 230 1.141 .96 70 2820 41080 44 51 210 217 0 783 41 741 .982 682 641 1.018 1.22 -.026 .287
9 1252 1608 64 50 1188 1558 954 1217 66 53 890 1167 0 0 967 1233 15 20 100 100 100 100 2746 2057 .763 1.311 1.311 1.317 1.285 1.767 52 334 1.315 .95 80 3060 41090 45 53 234 242 0 1307 41 1267 1.066 989 949 .938 1.066 .093 .092
10 314 456 66 52 248 404 171 226 68 54 105 174 0 0 254 417 14 12 96 100 93 100 652 279 .614 1.629 1.657 1.654 1.532 1.817 32 176 1.719 .83 60 3310 41090 46 52 260 266 0 371 42 328 1.324 184 141 .755 1.347 .405 .43
11 340 397 66 53 274 344 214 225 68 54 148 172 0 0 272 387 16 12 96 96 93 87 618 320 .797 1.255 1.162 1.029 1.125 3.7 32 176 1.486 .76 60 3560 41100 47 53 285 291 0 323 43 280 1.021 183 140 .98 .945 .03 -.082
12 664 689 70 58 594 631 652 725 74 62 582 667 0 0 243 261 25 22 100 100 100 100 1225 1249 .941 1.062 1.146 1.051 1.035 1.425 52 332 1.066 .95 80 3790 41080 44 52 307 315 0 560 47 513 .864 589 542 1.158 .932 -.211 -.102
13 473 587 69 57 404 530 308 436 71 57 239 379 0 0 415 461 16 13 96 98 96 98 934 618 .762 1.312 1.586 1.345 1.428 2.034 52 340 1.225 .9 80 4030 41090 45 53 331 339 0 477 46 431 1.067 354 308 .938 1.289 .093 .367
14 533 652 66 53 467 599 367 512 68 55 301 459 0 0 429 534 16 12 98 100 98 98 1066 760 .78 1.283 1.525 1.248 1.302 2.043 52 320 1.287 .91 80 4270 41070 43 51 355 363 0 530 43 487 1.043 416 373 .959 1.24 .06 .31
15 433 417 69 57 364 360 421 418 74 59 352 361 0 0 294 270 25 17 93 100 81 96 724 713 1.011 .989 1.026 1.236 .931 2.206 32 236 1.058 .89 70 4500 41080 44 51 378 385 0 339 46 293 .804 340 293 1.244 .834 -.315 -.262
16 395 657 72 56 323 601 176 275 79 61 104 219 0 0 510 591 52 30 91 100 50 100 924 323 .537 1.861 2.106 2.093 1.709 1.944 12 104 1.179 .76 50 4740 41080 45 50 403 408 0 534 46 489 1.513 224 178 .661 1.712 .597 .776
17 505 672 69 55 436 617 226 335 396 109 157 280 0 0 519 679 3418 424 0 40 0 25 1053 437 .707 1.415 1.783 1.535 1.612 1.999 32 236 1.458 .75 70 5000 41080 44 51 428 435 0 546 45 502 1.151 272 228 .869 1.45 .202 .536
18 510 447 74 50 436 397 348 327 75 52 274 277 0 0 420 388 19 12 100 96 90 84 833 551 1.098 .911 1.011 .826 .904 1.644 32 160 .942 .98 60 1150 41330 70 76 44 50 0 363 41 323 .74 266 225 1.351 .822 -.434 -.283
19 459 531 71 51 388 480 209 186 74 52 138 135 0 0 460 633 35 15 90 100 87 96 868 273 .808 1.237 .978 1.062 1.125 1.444 32 176 1.354 .97 60 1400 41330 70 76 69 75 0 432 41 390 1.006 151 110 .994 .795 .008 -.33
20 139 135 67 49 72 86 74 54 69 50 7 5 0 0 200 252 14 11 37 38 23 30 158 12 .837 1.194 .714 .993 .977 2.467 80 656 1.263 .95 110 1630 41330 67 78 89 100 -50 110 40 70 .971 44 4 1.03 .581 -.042 -.784

Total number of rows: 4608

Table truncated, full table size 1015 Kbytes.




Supplementary data files not provided
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