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Sample GSM150407 Query DataSets for GSM150407
Status Public on Dec 15, 2006
Title NSH57 9-5 1mo: S, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 9.3i; S, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 9.3i; 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 9-5 1mo; S, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 9-5 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, 34930; 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 = 36.79; Parameter Scan Time = 15:02:41; Parameter PMT Volts = 470; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49769; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.58; 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 = 36.79; Parameter Scan Time = 15:02:41; Parameter PMT Volts = 780; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49696; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.97; 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/2004-08/54737.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 99 219 59 176 40 43 78 175 62 219 19 -1 0 0 59 190 22 185 46 17 32 6 83 18 .93 1.075 null 3.614 4.111 6.198 156 1083 68.81 .07 150 2720 36050 104 119 127 142 -50 1399 1124 275 6.866 1118 -6 .146 null 2.779 null
2 123 241 58 185 65 56 120 229 60 221 62 44 0 0 55 175 16 178 73 25 60 6 121 106 1.161 .862 .71 2.854 2.879 3.852 80 511 58.326 .06 110 2910 36070 108 119 148 159 0 1539 1182 358 5.503 1463 281 .182 4.533 2.46 2.18
3 242 339 73 166 169 173 271 252 96 197 198 86 0 0 89 250 63 179 83 33 66 25 342 284 .977 1.024 .434 1.208 1.788 4.317 12 104 3.627 .42 50 3100 36030 107 112 170 175 0 2165 1060 1105 6.538 1610 549 .153 2.774 2.709 1.472
4 392 285 63 198 329 87 380 260 67 230 317 62 0 0 202 211 20 187 96 31 96 9 416 379 3.782 .264 .196 .736 .862 4.049 32 236 2.853 .06 70 3320 36060 109 116 191 198 0 1820 1265 556 1.689 1661 396 .592 1.249 .756 .321
5 313 305 66 191 247 114 314 206 74 231 248 15 0 0 192 285 40 177 86 34 71 19 361 263 2.167 .462 .06 .95 .844 3.946 52 420 4.321 .17 90 3520 36040 106 115 210 219 0 1948 1220 728 2.948 1316 96 .339 .386 1.56 -1.372
6 290 249 64 176 226 73 264 194 73 214 200 18 0 0 183 202 41 172 78 25 67 7 299 218 3.096 .323 .09 .778 .775 4.935 52 420 17.936 .03 90 3710 36030 105 114 229 238 0 1590 1124 466 2.063 1239 115 .485 .575 1.045 -.799
7 171 298 88 154 83 144 94 295 139 202 6 141 0 0 151 206 114 182 25 40 18 15 227 147 .576 1.735 23.5 5.779 2.967 6.902 32 176 -1 -1 60 3910 36080 112 118 251 257 0 1903 984 920 11.081 1884 901 .09 150.093 3.47 7.23
8 280 309 66 186 214 123 272 244 75 226 206 58 0 0 83 265 42 182 100 32 93 12 337 264 1.74 .575 .282 .571 .833 4.645 80 585 9.958 .12 110 4120 36050 106 117 269 280 0 1974 1188 786 3.671 1558 370 .272 1.798 1.876 .847
9 127 227 62 197 65 30 67 191 64 230 5 -6 0 0 119 177 20 182 37 16 30 5 95 -1 2.167 .462 null 3.486 4.828 7.6 156 946 -1 -1 150 4320 36040 103 118 287 302 -50 1450 1258 192 2.948 1220 -38 .339 null 1.56 null
10 134 213 61 185 73 28 77 186 72 226 16 1 0 0 103 162 50 189 34 16 28 4 101 17 2.607 .384 .063 2.788 3.077 6.802 156 991 -1 -1 150 4520 36040 103 118 307 322 -50 1360 1182 179 2.45 1188 6 .408 .399 1.293 -1.325
11 223 261 68 193 155 68 192 207 93 224 124 14 0 0 104 223 61 181 84 28 50 9 223 138 2.279 .439 .113 1.245 1.786 3.284 32 236 22.701 .08 70 4730 36050 108 115 332 339 0 1667 1233 434 2.802 1322 89 .357 .721 1.486 -.472
12 171 214 61 183 110 31 139 153 73 220 78 -30 0 0 102 195 48 184 64 16 42 7 141 48 3.548 .282 null 1.75 1.766 4.736 156 1089 51.033 .04 150 4920 36030 102 117 347 362 -50 1367 1169 198 1.8 977 -192 .556 null .848 null
13 240 241 62 177 178 64 233 186 78 224 171 9 0 0 67 202 52 195 96 21 92 11 242 180 2.781 .36 .053 .765 1.008 3.677 80 447 25.11 .05 100 5140 36030 105 115 372 382 0 1539 1130 409 2.296 1188 57 .435 .336 1.199 -1.573
14 138 252 61 169 77 83 135 187 78 215 74 18 0 0 52 211 67 185 58 28 12 9 160 92 .928 1.078 .243 2.243 2.287 4.79 156 969 92.721 .03 150 5320 36030 102 117 387 402 -50 1610 1079 530 6.885 1194 115 .145 1.554 2.783 .636
15 373 253 66 184 307 69 379 190 132 227 313 6 0 0 242 213 133 182 63 25 51 11 376 319 4.449 .225 .019 .403 .446 6.482 52 327 -1.326 -.05 80 5510 36010 104 112 410 418 0 1616 1175 441 1.435 1214 38 .697 .122 .522 -3.03
16 164 246 62 183 102 63 160 201 80 224 98 18 0 0 62 202 74 182 66 23 21 12 165 116 1.619 .618 .184 1.451 1.787 4.654 156 968 94.212 .03 150 5720 36030 102 117 427 442 -50 1571 1169 402 3.945 1284 115 .253 1.173 1.98 .23
17 111 210 60 194 51 16 72 156 61 228 12 -38 0 0 75 182 13 175 49 19 39 7 67 -26 3.188 .314 null 5.961 7.409 6.89 156 810 -50.929 -.07 150 5920 36030 102 117 447 462 -50 1341 1239 102 2.004 996 -243 .499 null 1.003 null
18 94 221 59 192 35 29 66 188 62 226 7 -4 0 0 64 171 26 177 33 17 25 5 64 3 1.207 .829 null 4.208 4.857 5.297 156 992 -1 -1 150 6120 36030 102 117 467 482 -50 1412 1226 185 5.292 1201 -26 .189 null 2.404 null
19 141 258 87 183 54 75 138 172 99 222 51 -11 0 0 33 205 50 170 50 25 8 25 129 40 .72 1.389 null 1.92 2.556 4.567 12 104 -65.902 -.03 50 2730 36220 126 131 133 138 0 1648 1169 479 8.871 1099 -70 .113 null 3.149 null
20 137 229 61 187 76 42 127 194 70 223 66 7 0 0 53 187 41 179 72 19 37 7 118 73 1.81 .553 .106 2 2.023 3.915 156 824 -1 -1 150 2920 36250 124 139 147 162 -50 1463 1194 268 3.53 1239 45 .283 .677 1.82 -.562

Total number of rows: 4992

Table truncated, full table size 1089 Kbytes.




Supplementary data files not provided
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