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Sample GSM480338 Query DataSets for GSM480338
Status Public on Oct 04, 2010
Title comB10 addA vs WT 1
Sample type RNA
 
Channel 1
Source name WT RNA
Organism Helicobacter pylori
Characteristics genotype: WT
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name msd23 RNA
Organism Helicobacter pylori
Characteristics genotype: comB10- addA- (msd23)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Scanner Model: GenePix 4000B
Description NSH57 WT and comB10- addA- cells were grown in Brucella Broth to OD600=0.7-0.9 and collected.
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81648.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 04, 2009
Last update date Oct 04, 2010
Contact name Nina Reda Salama
E-mail(s) nsalama@fhcrc.org
Phone 206-667-1540
Fax 206-667-6524
Organization name Fred Hutchinson Cancer Research Center
Department Division of Human Biology
Lab Mailstop C3-168
Street address 1100 Fairview Ave. N
City Seattle
State/province WA
ZIP/Postal code 19024
Country USA
 
Platform ID GPL9754
Series (1)
GSE19334 Dissecting the transcriptional response to DNA damage in Helicobacter pylori.

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
1 243 275 201 186 42 89 227 264 208 193 26 78 0 0 88 85 51 48 40 62 20 43 131 104 .472 2.119 3 1.387 1.331 3.096 80 656 .91 .39 110 2550 10140 80 91 37 48 0 291 197 94 2.244 280 83 .446 3.177 1.166 1.668
2 360 292 198 190 162 102 335 277 205 192 137 87 0 0 111 71 48 45 86 80 68 47 264 224 1.588 .63 .635 .584 .609 3.083 80 560 .605 .65 100 2800 10130 80 90 63 73 0 309 201 108 .667 293 92 1.5 .672 -.585 -.572
3 350 252 203 198 147 54 341 246 211 200 138 48 0 0 75 57 52 46 86 50 78 23 201 186 2.722 .367 .348 .346 .399 2.929 52 420 .443 .4 90 3050 10130 80 89 88 97 0 267 210 57 .389 260 51 2.571 .368 -1.362 -1.441
4 1514 1059 213 199 1301 860 1254 982 225 204 1041 783 0 0 834 444 120 53 100 100 95 97 2161 1824 1.513 .661 .752 .706 .702 1.497 80 560 .592 .94 100 3280 10120 79 89 111 121 0 1121 211 911 .7 1040 829 1.429 .796 -.515 -.328
5 342 373 226 218 116 155 327 368 237 225 101 150 0 0 91 104 103 75 50 80 15 49 271 251 .748 1.336 1.485 1.503 1.481 2.716 120 801 .413 .41 120 3520 10130 79 91 134 146 0 395 231 164 1.415 390 159 .707 1.573 .501 .653
6 995 834 223 215 772 619 933 828 231 222 710 613 0 0 383 216 85 76 97 100 96 98 1391 1323 1.247 .802 .863 .909 .826 1.734 80 656 .739 .92 110 3770 10120 78 89 159 170 0 883 228 655 .849 877 649 1.178 .914 -.236 -.129
7 642 726 238 226 404 500 646 725 269 231 408 499 0 0 157 185 361 65 57 100 2 100 904 907 .808 1.238 1.223 1.244 1.321 1.536 80 560 .907 .63 100 4020 10130 80 90 185 195 0 769 239 529 1.311 768 528 .763 1.295 .39 .373
8 415 380 238 229 177 151 363 335 241 232 125 106 0 0 195 130 55 59 71 73 53 43 328 231 1.172 .853 .848 .862 .844 2.528 80 656 .725 .71 110 4260 10120 78 89 208 219 0 402 242 160 .903 355 112 1.107 .898 -.147 -.155
9 390 355 239 230 151 125 369 343 247 234 130 113 0 0 92 88 58 53 86 78 58 56 276 243 1.208 .828 .869 .938 .9 2.248 80 656 .854 .56 110 4490 10120 78 89 231 242 0 376 244 132 .877 363 120 1.141 .92 -.19 -.12
10 623 431 215 214 408 217 574 408 221 218 359 194 0 0 223 102 49 48 100 98 98 91 625 553 1.88 .532 .54 .545 .539 1.664 80 560 .487 .85 100 4730 10120 79 89 256 266 0 456 227 230 .563 432 205 1.776 .572 -.828 -.805
11 322 321 227 227 95 94 289 291 236 231 62 64 0 0 127 115 58 56 51 51 35 40 189 126 1.011 .989 1.032 1.146 1.126 3.522 80 560 .984 .54 100 4980 10120 79 89 281 291 0 340 240 100 1.048 308 68 .954 1.093 .067 .128
12 596 610 245 242 351 368 413 599 251 248 168 357 0 0 553 131 68 66 77 100 57 98 719 525 .954 1.048 2.125 1.925 2.472 3.028 80 656 .305 .41 110 5210 10120 78 89 303 314 0 646 256 390 1.11 634 378 .901 2.25 .151 1.17
13 484 445 247 243 237 202 479 445 251 248 232 202 0 0 86 80 69 52 98 98 86 90 439 434 1.173 .852 .871 .851 .865 1.702 80 656 .837 .72 110 5450 10110 77 88 327 338 0 471 257 214 .903 471 214 1.108 .922 -.148 -.117
14 1875 1863 224 229 1651 1634 1698 1720 231 236 1474 1491 0 0 1206 1003 50 53 100 100 100 100 3285 2965 1.01 .99 1.012 1.126 1.092 1.511 80 560 .913 .95 100 5690 10110 78 88 352 362 0 1973 242 1730 1.048 1821 1579 .954 1.071 .068 .099
15 12905 14613 230 231 12675 14382 12555 15525 233 236 12325 15294 0 0 7277 6805 59 51 100 100 100 100 27057 27619 .881 1.135 1.241 1.241 1.166 1.396 80 560 1.066 .97 100 5930 10120 79 89 376 386 0 15474 245 15229 1.202 16440 16195 .832 1.314 .265 .394
16 418 409 240 247 178 162 411 400 246 251 171 153 0 0 111 116 52 54 85 82 71 63 340 324 1.099 .91 .895 .895 1.002 2.834 80 650 .944 .64 110 6180 10120 78 89 400 411 0 433 262 172 .964 424 162 1.038 .947 -.053 -.078
17 384 386 256 256 128 130 360 371 262 261 104 115 0 0 118 120 59 57 70 71 45 50 258 219 .985 1.016 1.106 1.024 1.067 2.753 120 794 .979 .56 120 6410 10120 78 90 423 435 0 409 271 138 1.075 393 122 .93 1.171 .105 .228
18 325 346 212 202 113 144 308 328 220 207 96 126 0 0 81 92 54 52 80 88 44 67 257 222 .785 1.274 1.313 1.235 1.152 1.998 52 340 1.206 .5 80 2590 10380 106 114 43 51 0 366 214 152 1.349 347 133 .741 1.39 .432 .475
19 259 248 206 201 53 47 244 234 211 207 38 33 0 0 105 101 49 51 37 37 18 23 100 71 1.128 .887 .868 .949 1.082 3.028 80 560 .948 .6 100 2830 10360 103 113 66 76 0 263 213 50 .939 248 35 1.065 .92 -.091 -.121
20 588 521 205 202 383 319 525 497 210 207 320 295 0 0 207 151 47 49 100 98 98 93 702 615 1.201 .833 .922 .845 .862 1.604 80 656 .797 .86 110 3060 10360 102 113 88 99 0 552 214 338 .882 526 312 1.134 .976 -.181 -.035

Total number of rows: 4032

Table truncated, full table size 888 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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