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Sample GSM150392 Query DataSets for GSM150392
Status Public on Dec 15, 2006
Title NSH57 20-1 1mo: N3, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 20.1i; N3, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 20.1i; 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 20-1 1mo; N3, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 20-1 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 = 1440, 8210; 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 = 30.32; Parameter Scan Time = 10:51:40; Parameter PMT Volts = 450; Parameter Scan Date = 2005-02-16; Parameter Pixel Size = 10; Parameter Laser on time = 58540; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.50; 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 = 30.32; Parameter Scan Time = 10:51:40; Parameter PMT Volts = 700; Parameter Scan Date = 2005-02-16; Parameter Pixel Size = 10; Parameter Laser on time = 58287; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.72; 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/2005-02/59523.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
1 255 157 142 124 113 33 237 163 151 154 95 39 0 0 91 101 73 121 56 15 21 3 146 134 3.424 .292 .411 .509 .836 4.836 32 176 -1.789 -.08 60 2190 10030 179 185 72 78 0 764 604 161 1.422 794 190 .703 1.999 .508 .999
2 252 168 149 121 103 47 236 152 153 145 87 31 0 0 108 125 46 109 66 25 47 10 150 118 2.191 .456 .356 1.087 1.038 5.112 80 585 10.077 .09 110 2400 10010 174 185 90 101 0 818 589 229 2.221 740 151 .45 1.735 1.151 .795
3 197 167 148 122 49 45 177 142 151 144 29 20 0 0 67 115 29 103 48 26 28 10 94 49 1.089 .918 .69 1.645 1.897 5.614 120 537 15.712 .11 120 2590 10040 177 189 109 121 0 813 594 219 4.471 691 97 .224 3.357 2.161 1.747
4 164 154 149 123 15 31 164 134 154 143 15 11 0 0 31 117 35 106 23 19 5 6 46 26 .484 2.067 .733 2.104 2.802 4.647 156 949 -1 -1 150 2790 10000 171 186 127 142 -50 750 599 151 10.061 652 54 .099 3.57 3.331 1.836
5 244 140 172 106 72 34 250 132 196 130 78 26 0 0 83 117 72 107 58 33 25 8 106 104 2.118 .472 .333 1.395 1.36 2.262 12 104 10.561 .05 50 3020 9990 175 180 155 160 0 682 516 166 2.299 643 127 .435 1.623 1.201 .698
6 241 152 154 119 87 33 212 104 159 138 58 -15 0 0 91 125 38 101 71 31 46 12 120 43 2.636 .379 null 1.876 2.294 2.805 32 236 40.463 .03 70 3180 9980 173 180 170 177 0 740 579 161 1.847 506 -73 .542 null .885 null
7 188 149 150 123 38 26 167 134 155 140 17 11 0 0 74 103 36 106 39 21 26 7 64 28 1.462 .684 .647 1.87 2 4.963 156 1087 23.854 .07 150 3400 10000 171 186 188 203 -50 725 599 127 3.331 652 54 .3 3.15 1.736 1.655
8 234 189 152 126 82 63 230 163 164 138 78 37 0 0 55 104 51 101 65 30 30 13 145 115 1.302 .768 .474 .806 .755 3.271 52 316 -1 -1 80 3620 9990 174 182 214 222 0 920 613 307 3.74 794 180 .267 2.309 1.903 1.207
9 165 146 156 117 9 29 154 121 159 141 -2 4 0 0 55 106 30 105 21 18 14 5 38 2 .31 3.222 null 2.319 2.458 5.029 156 997 -70.372 -.03 150 3800 10000 171 186 228 243 -50 711 570 141 15.687 589 19 .064 null 3.971 null
10 229 196 152 114 77 82 228 172 158 135 76 58 0 0 43 128 31 97 87 31 62 15 159 134 .939 1.065 .763 1.138 1.474 2.789 32 231 8.422 .19 70 3980 10010 176 183 250 257 0 954 555 399 5.184 837 282 .193 3.715 2.374 1.893
11 223 158 151 121 72 37 185 130 158 144 34 9 0 0 298 120 41 110 48 19 24 6 109 43 1.946 .514 .265 1.66 1.724 6.998 156 1140 -1 -1 150 4200 10000 171 186 268 283 -50 769 589 180 2.502 633 44 .4 1.289 1.323 .366
12 188 172 177 124 11 48 176 192 223 161 -1 68 0 0 62 117 347 135 0 16 0 8 59 67 .229 4.364 null 2.489 1.526 5.371 12 104 .886 .24 50 4390 10010 177 182 292 297 0 837 604 234 21.243 935 331 .047 null 4.409 null
13 286 162 158 111 128 51 249 148 174 139 91 37 0 0 166 106 53 106 81 25 40 6 179 128 2.51 .398 .407 .919 .994 3.119 32 236 .4 .05 70 4570 10000 175 182 309 316 0 789 540 248 1.94 720 180 .516 1.979 .956 .985
14 227 169 164 119 63 50 213 143 174 142 49 24 0 0 93 121 43 107 56 31 28 12 113 73 1.26 .794 .49 1.882 1.444 3.769 32 204 8.568 .12 70 4850 9990 174 181 337 344 0 823 579 243 3.864 696 117 .259 2.384 1.95 1.254
15 208 168 152 119 56 49 198 149 157 141 46 30 0 0 71 116 34 103 57 26 35 9 105 76 1.143 .875 .652 1.78 1.83 4.207 156 956 29.641 .05 150 5000 10000 171 186 348 363 -50 818 579 239 4.26 725 146 .235 3.175 2.091 1.667
16 241 152 153 129 88 23 221 150 163 151 68 21 0 0 82 108 102 106 33 15 10 7 111 89 3.826 .261 .309 .935 .935 3.799 80 526 6.973 .09 100 5230 10000 174 184 374 384 0 740 628 112 1.272 730 102 .786 1.503 .348 .588
17 236 152 148 128 88 24 210 118 160 146 62 -10 0 0 83 110 142 106 21 25 3 6 112 52 3.667 .273 null 1.493 1.359 2.962 32 230 -.056 -.05 70 5390 10000 175 182 391 398 0 740 623 117 1.328 574 -49 .753 null .409 null
18 177 136 151 120 26 16 161 111 154 144 10 -9 0 0 59 91 37 103 35 14 15 4 42 1 1.625 .615 null 1.847 2.273 3.605 156 1188 -1 -1 150 5600 10000 171 186 408 423 -50 662 584 78 2.996 540 -44 .334 null 1.583 null
19 213 181 151 120 62 61 204 162 156 144 53 42 0 0 53 110 37 116 61 25 38 7 123 95 1.016 .984 .792 1.4 2.061 4.358 52 304 17.923 .09 80 2200 10230 198 206 72 80 0 881 584 297 4.79 789 204 .209 3.858 2.26 1.948
20 230 172 149 118 81 54 223 146 154 138 74 28 0 0 70 127 32 106 73 26 57 9 135 102 1.5 .667 .378 1.239 1.242 4.895 120 632 12.585 .12 120 2410 10220 195 207 91 103 0 837 574 263 3.245 711 136 .308 1.842 1.698 .881

Total number of rows: 4992

Table truncated, full table size 1058 Kbytes.




Supplementary data files not provided
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