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Sample GSM150429 Query DataSets for GSM150429
Status Public on Dec 15, 2006
Title NSH57 11-5 1mo: S, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 11.3i; S, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 11.3i; 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 11-5 1mo; S, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 11-5 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 = 870, 9190; 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 = 37.99; Parameter Scan Time = 15:23:40; Parameter PMT Volts = 510; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 73696; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47267]; Parameter Laser Power = 1.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; 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 = 37.99; Parameter Scan Time = 15:23:40; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 67625; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47267]; Parameter Laser Power = 1.41; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin
Description Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54740.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
1 131 72 52 50 79 22 113 67 54 55 61 17 0 0 70 33 16 21 86 40 65 21 101 78 3.591 .278 .279 .392 .381 2.458 52 340 .234 .36 80 2360 10330 110 118 145 153 0 101 70 31 .393 94 24 2.548 .393 -1.349 -1.348
2 172 141 51 51 121 90 102 125 53 54 51 74 0 0 145 66 14 22 82 90 69 71 211 125 1.344 .744 1.451 .952 .924 3.119 120 663 .477 .67 120 2580 10360 111 123 165 177 0 199 72 127 1.048 176 104 .954 2.045 .068 1.032
3 295 122 51 50 244 72 196 112 54 55 145 62 0 0 272 64 26 23 73 75 66 60 316 207 3.389 .295 .428 .431 .33 2.858 120 628 .216 .76 120 2780 10360 111 123 185 197 0 172 70 101 .416 158 87 2.404 .603 -1.266 -.731
4 361 108 51 52 310 56 306 87 56 55 255 35 0 0 320 67 28 24 82 57 68 45 366 290 5.536 .181 .137 .254 .194 3.082 80 535 .161 .72 110 2980 10350 110 121 205 216 0 152 73 79 .255 123 49 3.927 .193 -1.974 -2.37
5 288 181 52 52 236 129 175 163 55 56 123 111 0 0 251 79 20 24 88 93 76 86 365 234 1.829 .547 .902 .856 .718 2.641 120 717 .372 .78 130 3170 10350 109 122 223 236 0 255 73 182 .77 230 156 1.298 1.272 -.376 .347
6 125 95 52 53 73 42 112 88 54 58 60 35 0 0 64 44 18 25 78 62 60 34 115 95 1.738 .575 .583 .6 .588 3.101 120 653 .547 .6 120 3380 10350 110 122 245 257 0 134 75 59 .811 124 49 1.233 .822 -.302 -.282
7 118 174 53 60 65 114 105 130 55 67 52 70 0 0 61 136 16 39 75 64 59 45 179 122 .57 1.754 1.346 1.634 1.796 2.997 120 624 2.49 .73 120 3580 10360 111 123 265 277 0 245 85 161 2.472 183 99 .405 1.897 1.306 .924
8 4548 57306 56 81 4492 57225 4603 62958 59 112 4547 62877 0 45 1156 10962 18 98 100 100 100 100 61717 67424 .078 12.739 13.828 12.979 12.984 1.281 156 803 12.821 .97 140 3790 10360 110 124 285 299 0 80774 114 80660 17.956 88741 88627 .056 19.491 4.166 4.285
9 453 3679 55 86 398 3593 78 287 58 115 23 201 0 0 677 6273 18 93 53 59 43 51 3991 224 .111 9.028 8.739 7.873 8.583 3.09 156 871 9.711 .93 150 3990 10340 107 122 304 319 -50 5186 121 5064 12.725 405 283 .079 12.318 3.67 3.623
10 249 1268 51 74 198 1194 150 863 53 81 99 789 0 0 222 1339 16 39 89 91 85 82 1392 888 .166 6.03 7.97 4.797 5.399 2.6 120 660 6.59 .91 130 4190 10350 109 122 325 338 0 1787 104 1683 8.5 1216 1112 .118 11.234 3.087 3.49
11 161 533 49 61 112 472 118 303 51 65 69 242 0 0 102 550 15 27 90 93 82 78 584 311 .237 4.214 3.507 2.955 3.5 2.346 120 677 5.391 .87 130 4380 10350 109 122 344 357 0 751 86 665 5.94 427 341 .168 4.944 2.57 2.306
12 139 282 49 56 90 226 105 127 51 60 56 71 0 0 87 328 14 25 88 68 75 55 316 127 .398 2.511 1.268 1.681 2.307 3.137 120 621 3.761 .86 120 4590 10350 110 122 366 378 0 397 79 319 3.539 179 100 .283 1.787 1.824 .838
13 145 181 50 56 95 125 137 169 52 59 87 113 0 0 42 65 13 28 100 97 98 87 220 200 .76 1.316 1.299 1.218 1.289 2.135 156 766 1.531 .76 140 4790 10350 109 123 385 399 0 255 79 176 1.855 238 159 .539 1.831 .891 .872
14 103 149 51 55 52 94 101 144 53 58 50 89 0 0 30 53 15 23 89 92 75 83 146 139 .553 1.808 1.78 1.809 1.814 2.135 156 730 2.243 .69 140 5000 10350 109 123 406 420 0 210 78 132 2.548 203 125 .392 2.509 1.349 1.327
15 8425 1100 55 54 8370 1046 7784 960 63 57 7729 906 0 0 3004 439 31 23 100 100 100 100 9416 8635 8.002 .125 .117 .123 .123 1.306 156 666 .123 .95 150 5200 10360 109 124 425 440 0 1550 76 1474 .176 1353 1277 5.677 .165 -2.505 -2.597
16 193 141 55 56 138 85 151 125 64 60 96 69 0 0 130 68 45 39 86 73 53 45 223 165 1.624 .616 .719 .631 .646 2.791 208 987 .436 .61 160 5380 10360 109 125 443 459 0 199 79 120 .868 176 97 1.152 1.013 -.204 .019
17 389 130 52 52 337 78 285 102 54 55 233 50 0 0 317 86 18 24 90 63 82 51 415 283 4.321 .231 .215 .258 .311 2.237 52 376 .24 .83 90 5620 10340 110 119 470 479 0 183 73 110 .326 144 70 3.065 .302 -1.616 -1.725
18 375 153 50 50 325 103 254 100 53 53 204 50 0 0 404 139 15 23 84 65 82 51 428 254 3.155 .317 .245 .307 .283 4.371 52 368 .318 .8 90 5770 10360 112 121 485 494 0 216 70 145 .447 141 70 2.239 .345 -1.163 -1.533
19 159 92 54 52 105 40 116 77 55 56 62 25 0 0 104 49 16 23 80 50 70 35 145 87 2.625 .381 .403 .44 .386 2.952 120 684 .336 .58 120 2390 10560 131 143 146 158 0 130 73 56 .537 109 35 1.862 .568 -.897 -.815
20 229 150 52 50 177 100 209 145 54 53 157 95 0 0 112 57 15 23 99 89 94 79 277 252 1.77 .565 .605 .586 .6 2.348 120 593 .501 .74 130 2600 10550 129 142 166 179 0 211 70 141 .796 204 134 1.256 .853 -.329 -.23

Total number of rows: 4992

Table truncated, full table size 1020 Kbytes.




Supplementary data files not provided
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