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Sample GSM150399 Query DataSets for GSM150399
Status Public on Dec 15, 2006
Title NSH57 9-1 1mo: N3, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 9.1i; N3, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 9.1i; N3, 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; N3, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 9-1 1mo; N3, 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 = 1210, 8590; 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 = 36.18; Parameter Scan Time = 14:28:54; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49741; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.51; 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 = 36.18; Parameter Scan Time = 14:28:54; Parameter PMT Volts = 760; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49668; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.92; 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/2004-08/54730.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 93 241 78 191 15 50 83 202 80 227 5 11 0 0 36 184 18 168 35 21 23 9 65 16 .3 3.333 2.2 6.508 5.684 4.608 156 964 80.776 .08 150 2400 9790 112 127 111 126 -50 304 241 63 4.198 254 14 .238 2.771 2.07 1.47
2 99 239 80 196 19 43 93 200 84 234 13 4 0 0 31 173 25 177 35 18 14 6 62 17 .442 2.263 .308 5.221 6.088 4.852 156 871 164.278 .03 150 2600 9790 112 127 131 146 -50 301 247 54 2.85 252 5 .351 .388 1.511 -1.368
3 119 216 80 193 39 23 113 181 82 225 33 -12 0 0 40 158 19 171 66 14 46 5 62 21 1.696 .59 null 3.273 3.455 5.736 156 809 74.152 .06 150 2800 9790 112 127 151 166 -50 272 243 29 .743 228 -15 1.346 null -.429 null
4 120 239 82 184 38 55 106 209 86 217 24 25 0 0 51 168 26 158 46 19 27 6 93 49 .691 1.447 1.042 3.343 3.842 3.946 156 882 81.393 .05 150 3000 9790 112 127 171 186 -50 301 232 69 1.823 263 31 .549 1.312 .866 .392
5 121 224 83 183 38 41 109 190 85 218 26 7 0 0 50 171 24 165 51 20 32 8 79 33 .927 1.079 .269 3.337 4.182 5.897 156 959 -1 -1 150 3200 9780 111 126 191 206 -50 282 230 52 1.359 239 9 .736 .339 .442 -1.56
6 149 273 102 211 47 62 112 223 112 249 10 12 0 0 119 178 43 188 33 25 16 8 109 22 .758 1.319 1.2 3.493 4.344 2.004 12 104 -1 -1 50 3390 9810 119 124 215 220 0 344 266 78 1.661 281 15 .602 1.511 .732 .596
7 107 220 82 193 25 27 103 185 85 231 21 -8 0 0 27 163 24 174 45 18 22 3 52 13 .926 1.08 null 4.444 4.148 4.523 156 931 223.931 .03 150 3600 9780 111 126 231 246 -50 277 243 34 1.36 233 -10 .735 null .444 null
8 128 258 82 179 46 79 127 220 84 219 45 41 0 0 36 163 20 168 73 26 54 9 125 86 .582 1.717 .911 2.393 2.777 4.44 156 863 72.012 .07 150 3800 9780 111 126 251 266 -50 325 225 100 2.163 277 52 .462 1.148 1.113 .199
9 104 228 82 182 22 46 89 186 84 213 7 4 0 0 51 184 18 160 39 21 26 8 68 11 .478 2.091 .571 5.534 5.357 4.754 156 806 -1 -1 150 4010 9770 110 125 272 287 -50 287 229 58 2.634 234 5 .38 .72 1.397 -.474
10 105 215 83 194 22 21 102 175 86 217 19 -19 0 0 28 174 21 157 44 20 24 7 43 0 1.048 .955 null 5.813 6.4 3.884 156 913 242.14 .03 150 4210 9770 110 125 292 307 -50 271 244 26 1.202 220 -24 .832 null .266 null
11 123 248 87 198 36 50 119 194 94 202 32 -4 0 0 30 186 30 136 50 28 18 18 86 28 .72 1.389 null 3.032 3.961 4.623 32 170 90.083 .05 60 4440 9810 119 125 320 326 0 312 249 63 1.749 244 -5 .572 null .807 null
12 110 228 87 191 23 37 105 196 92 225 18 5 0 0 34 170 28 167 36 22 16 7 60 23 .622 1.609 .278 4.448 4.683 5.342 156 1073 184.695 .03 150 4610 9770 110 125 332 347 -50 287 241 47 2.026 247 6 .494 .35 1.019 -1.515
13 173 362 99 222 74 140 185 380 105 257 86 158 0 0 38 206 37 186 66 50 58 25 214 244 .529 1.892 1.837 4.253 3.99 1.898 12 104 28.446 .11 50 4830 9750 113 118 359 364 0 456 280 176 2.383 479 199 .42 2.314 1.253 1.21
14 119 235 85 198 34 37 117 212 89 230 32 14 0 0 34 171 25 169 54 22 30 5 71 46 .919 1.088 .438 4.068 4.227 3.906 156 1016 120.876 .04 150 5010 9760 109 124 372 387 -50 296 249 47 1.371 267 18 .73 .551 .455 -.86
15 117 225 85 188 32 37 115 219 87 219 30 31 0 0 38 142 23 159 54 18 30 3 69 61 .865 1.156 1.033 2.773 2.938 4.289 156 854 180.236 .03 150 5210 9760 109 124 392 407 -50 283 237 47 1.456 276 39 .687 1.302 .542 .38
16 158 333 86 191 72 142 152 254 91 227 66 63 0 0 59 402 27 163 77 35 62 17 214 129 .507 1.972 .955 2.972 3.356 4.047 80 439 11.974 .39 100 5420 9770 113 123 416 426 0 419 241 179 2.484 320 79 .403 1.202 1.313 .266
17 104 244 81 190 23 54 92 208 83 226 11 18 0 0 42 181 19 175 41 19 25 7 77 29 .426 2.348 1.636 4.839 4.98 4.295 156 831 92.707 .07 150 5610 9750 108 123 432 447 -50 307 239 68 2.957 262 23 .338 2.061 1.564 1.043
18 93 238 82 191 11 47 88 193 84 224 6 2 0 0 32 186 18 170 33 22 17 8 58 8 .234 4.273 .333 6.292 6.474 3.525 156 950 115.464 .05 150 5810 9750 108 123 452 467 -50 300 241 59 5.382 243 3 .186 .42 2.428 -1.252
19 111 233 81 191 30 42 109 195 86 226 28 4 0 0 28 182 25 163 55 21 25 8 72 32 .714 1.4 .143 4.704 4.737 4.4 156 963 207.454 .03 150 2400 9990 132 147 111 126 -50 293 241 53 1.763 246 5 .567 .18 .818 -2.474
20 124 275 94 220 30 55 114 229 104 252 20 9 0 0 39 196 39 179 37 18 12 12 85 29 .545 1.833 .45 2.312 2.526 5.449 32 176 30.588 .15 60 2590 10000 138 144 135 141 0 346 277 69 2.309 288 11 .433 .567 1.207 -.819

Total number of rows: 4992

Table truncated, full table size 1058 Kbytes.




Supplementary data files not provided
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