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Sample GSM150400 Query DataSets for GSM150400
Status Public on Dec 15, 2006
Title NSH57 9-1 1mo: S, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 9.1i; S, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 9.1i; S, 2C
Extracted molecule genomic DNA
Extraction protocol pubmed ID 17101654
Label Cy3
Label protocol pubmed ID 17101654
 
Channel 2
Source name output mouse NSH57 9-1 1mo; S, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 9-1 1mo; S, 2C
Extracted molecule genomic DNA
Extraction protocol pubmed ID 17101654
Label Cy5
Label protocol pubmed ID 17101654
 
 
Hybridization protocol pubmed ID 17101654
Scan protocol pubmed ID 17101654
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1370, 34940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.25; Parameter Scan Time = 14:31:27; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49744; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.25; Parameter Scan Time = 14:31:27; Parameter PMT Volts = 700; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49670; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.91; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin
Description Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54731.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 14, 2006
Last update date Jan 03, 2007
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 GPL2781
Series (2)
GSE6528 NSH57 Tn Library Mouse Pools
GSE6531 Identification of Helicobacter pylori genes contributing to stomach colonization.

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
1 163 166 82 106 81 60 152 139 87 130 70 33 0 0 47 107 45 114 75 28 40 6 141 103 1.35 .741 .471 .912 1.185 3.428 32 176 13.828 .11 60 2460 36180 121 127 106 112 0 254 162 92 1.134 213 51 .882 .721 .181 -.471
2 113 122 84 97 29 25 106 99 88 120 22 2 0 0 43 85 31 95 41 23 21 3 54 24 1.16 .862 .091 2.239 2.22 4.631 156 1140 37.767 .07 150 2690 36160 114 129 124 139 -50 187 148 38 1.319 152 3 .758 .139 .4 -2.846
3 131 131 93 102 38 29 129 99 101 124 36 -3 0 0 34 102 37 92 43 21 15 9 67 33 1.31 .763 null 1.153 1.457 4.093 32 176 20.809 .09 60 2930 36170 120 126 153 159 0 200 156 44 1.168 152 -5 .856 null .224 null
4 166 158 83 100 83 58 160 116 92 124 77 16 0 0 78 104 54 92 61 32 30 13 141 93 1.431 .699 .208 .901 .972 5.468 52 340 5.109 .09 80 3100 36140 116 124 169 177 0 242 153 89 1.069 178 24 .935 .318 .097 -1.653
5 132 169 95 108 37 61 119 145 104 134 24 37 0 0 42 107 42 107 43 28 12 9 98 61 .607 1.649 1.542 2.32 2.51 3.294 32 176 -37.98 -.04 60 3310 36160 119 125 191 197 0 259 165 93 2.523 222 57 .396 2.359 1.335 1.238
6 122 129 88 106 34 23 107 111 94 125 19 5 0 0 50 87 46 88 33 21 14 6 57 24 1.478 .676 .263 2.105 1.97 4.286 156 944 -1 -1 150 3490 36150 113 128 204 219 -50 197 162 35 1.035 170 8 .966 .403 .05 -1.312
7 369 515 84 104 285 411 122 115 90 123 38 11 0 0 1831 2535 45 89 41 28 16 12 696 49 .693 1.442 .289 1.919 2.37 6.911 156 903 2.156 .39 150 3700 36150 113 128 225 240 -50 788 159 629 2.207 176 17 .453 .443 1.142 -1.175
8 184 156 84 102 100 54 178 132 94 125 94 30 0 0 51 105 71 120 70 24 18 8 154 124 1.852 .54 .319 .741 .806 3.63 120 624 3.043 .35 120 3900 36170 117 129 247 259 0 239 156 83 .826 202 46 1.21 .488 -.275 -1.034
9 215 144 83 87 132 57 206 118 86 114 123 31 0 0 98 96 45 135 76 19 57 1 189 154 2.316 .432 .252 .677 .688 4.711 52 375 3.512 .07 90 4060 36140 115 124 264 273 0 220 133 87 .661 181 47 1.513 .386 -.598 -1.374
10 206 180 88 111 118 69 207 175 102 131 119 64 0 0 53 119 49 89 91 33 75 16 187 183 1.71 .585 .538 .639 .845 3.378 12 104 22.961 .05 50 4270 36130 116 121 287 292 0 275 170 106 .895 268 98 1.117 .823 -.16 -.281
11 158 163 84 105 74 58 155 144 87 125 71 39 0 0 46 94 22 89 86 31 70 16 132 110 1.276 .784 .549 1.176 1.049 4.11 80 526 7.047 .22 100 4490 36150 116 126 307 317 0 249 161 89 1.199 220 60 .834 .841 .262 -.25
12 148 167 94 105 54 62 144 139 102 125 50 34 0 0 43 125 37 87 65 28 34 18 116 84 .871 1.148 .68 2.322 2.27 2.722 32 236 10.368 .17 70 4670 36150 117 124 326 333 0 256 161 95 1.757 213 52 .569 1.041 .813 .057
13 201 241 84 104 117 137 193 211 89 125 109 107 0 0 52 151 25 88 97 52 91 37 254 216 .854 1.171 .982 1.031 1.274 3.481 120 718 4.045 .38 120 4900 36160 116 128 347 359 0 369 159 210 1.792 323 164 .558 1.502 .842 .587
14 150 191 85 111 65 80 150 172 88 129 65 61 0 0 41 113 24 89 82 41 62 18 145 126 .813 1.231 .938 1.479 1.649 3.909 80 584 8.941 .22 110 5100 36150 115 126 367 378 0 292 170 122 1.884 263 93 .531 1.436 .913 .522
15 157 146 87 111 70 35 138 135 96 132 51 24 0 0 124 94 44 101 56 19 26 4 105 75 2 .5 .471 1.135 1.108 4.513 156 1086 -1 -1 150 5310 36150 113 128 386 401 -50 223 170 54 .765 207 37 1.307 .72 -.386 -.474
16 155 208 98 112 57 96 161 169 113 123 63 57 0 0 49 110 49 91 58 33 25 25 153 120 .594 1.684 .905 1.119 1.039 2.593 12 104 -1 -1 50 5550 36120 115 120 415 420 0 318 171 147 2.577 259 87 .388 1.385 1.366 .469
17 124 185 101 122 23 63 116 182 110 137 15 60 0 0 58 154 42 92 25 33 16 25 86 75 .365 2.739 4 3.275 3.516 2.843 12 104 18.808 .09 50 5770 36190 122 127 437 442 0 283 187 96 4.192 279 92 .239 6.122 2.068 2.614
18 186 160 81 100 105 60 184 152 83 119 103 52 0 0 58 85 21 84 92 38 82 11 165 155 1.75 .571 .505 .853 .938 3.863 52 332 4.112 .2 80 5920 36150 117 125 451 459 0 245 153 92 .875 233 80 1.144 .773 -.193 -.372
19 126 125 84 98 42 27 125 108 88 120 41 10 0 0 44 90 31 93 57 16 33 5 69 51 1.556 .643 .244 1.404 1.318 4.429 156 1076 38.476 .05 150 2490 36360 134 149 104 119 -50 191 150 41 .984 165 15 1.016 .373 -.024 -1.422
20 148 151 92 99 56 52 138 128 105 124 46 29 0 0 48 114 41 89 56 31 18 12 108 75 1.077 .929 .63 2.087 1.558 2.915 32 176 12.4 .14 60 2740 36350 138 144 134 140 0 231 152 80 1.421 196 44 .704 .965 .507 -.052

Total number of rows: 4992

Table truncated, full table size 1059 Kbytes.




Supplementary data files not provided
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