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Sample GSM150526 Query DataSets for GSM150526
Status Public on Dec 15, 2006
Title NSH57 15-4 1wk: S, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 15.2i; S, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 15.2i; 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 15-4 1wk; S, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 15-4 1wk; 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 = 990, 9390; 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 = 32.28; Parameter Scan Time = 11:46:17; Parameter PMT Volts = 470; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 49423; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.43; 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 = 32.28; Parameter Scan Time = 11:46:17; Parameter PMT Volts = 690; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 49349; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.80; 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/2004-08/54702.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 95 140 72 109 23 31 81 118 75 124 9 9 0 0 49 120 22 84 32 19 17 9 54 18 .742 1.348 1 3.1 3.746 4.292 156 1132 14.361 .2 150 2350 10250 78 93 128 143 -50 150 116 33 1.439 126 10 .695 1.068 .526 .095
2 422 238 72 101 350 137 377 212 74 121 305 111 0 0 210 156 17 86 99 53 99 31 487 416 2.555 .391 .364 .394 .463 3.056 120 721 .441 .45 130 2550 10250 79 92 149 162 0 254 108 146 .418 226 119 2.392 .389 -1.258 -1.363
3 182 170 71 107 111 63 192 177 74 129 121 70 0 0 78 97 21 92 84 38 76 9 174 191 1.762 .568 .579 1.295 .877 4.536 52 397 5.241 .18 90 2730 10230 79 88 169 178 0 182 114 67 .606 189 75 1.65 .618 -.722 -.695
4 197 189 80 100 117 89 198 159 90 121 118 59 0 0 52 95 40 89 91 41 83 16 206 177 1.315 .761 .5 .743 .726 3.241 12 104 3.699 .3 50 2940 10220 80 85 192 197 0 202 107 95 .812 170 63 1.231 .534 -.3 -.905
5 266 306 78 97 188 209 265 270 82 115 187 173 0 0 90 159 23 77 100 81 90 56 397 360 .9 1.112 .925 1.142 .968 2.736 32 176 2.363 .33 60 3150 10230 81 87 213 219 0 327 104 223 1.187 288 185 .842 .988 .248 -.017
6 174 197 74 102 100 95 159 166 77 119 85 64 0 0 78 145 26 88 80 44 69 21 195 149 1.053 .95 .753 1.035 1.026 3.268 52 382 4.231 .25 90 3360 10280 84 93 232 241 0 210 109 101 1.015 177 68 .986 .804 .021 -.314
7 164 197 72 97 92 100 152 173 74 113 80 76 0 0 75 117 16 82 78 47 71 28 192 156 .92 1.087 .95 1.434 1.709 4.479 80 511 4.377 .29 100 3550 10250 81 91 251 261 0 210 104 107 1.161 185 81 .861 1.015 .215 .021
8 377 257 72 104 305 153 383 235 73 118 311 131 0 0 144 146 16 79 100 68 100 41 458 442 1.993 .502 .421 .477 .531 2.863 120 753 .61 .54 130 3760 10260 80 93 270 283 0 274 111 163 .536 251 140 1.867 .45 -.9 -1.152
9 301 282 69 105 232 177 292 240 70 117 223 135 0 0 165 191 15 75 96 68 90 46 409 358 1.311 .763 .605 .728 .667 3.713 32 224 1.065 .52 70 3920 10270 84 91 289 296 0 301 112 189 .815 256 144 1.227 .647 -.295 -.629
10 161 182 70 94 91 88 149 159 71 117 79 65 0 0 72 115 14 85 86 45 80 18 179 144 1.034 .967 .823 1.294 1.33 3.983 80 510 8.177 .16 100 4160 10250 81 91 312 322 0 194 100 94 1.033 170 69 .968 .879 .047 -.187
11 166 185 71 107 95 78 162 164 105 134 91 57 0 0 61 116 529 200 0 16 0 0 173 148 1.218 .821 .626 1.043 1.014 2.783 120 635 3.711 .37 120 4350 10250 80 92 330 342 0 198 114 83 .877 175 61 1.14 .669 -.19 -.58
12 130 183 69 101 61 82 124 163 72 116 55 62 0 0 56 111 16 81 72 46 63 26 143 117 .744 1.344 1.127 2.091 2.049 3.736 80 500 5.342 .29 100 4540 10240 80 90 350 360 0 195 108 88 1.436 174 66 .697 1.204 .522 .268
13 147 201 72 103 75 98 143 182 74 122 71 79 0 0 44 112 21 86 90 49 69 25 173 150 .765 1.307 1.113 1.514 1.539 3.499 120 824 6.222 .34 130 4740 10240 78 91 368 381 0 215 110 105 1.396 194 84 .717 1.188 .481 .249
14 116 168 72 106 44 62 113 140 74 124 41 34 0 0 34 118 17 83 75 37 55 13 106 75 .71 1.409 .829 1.959 2.383 4.71 80 508 18.365 .15 100 4950 10230 79 89 391 401 0 179 113 66 1.505 150 36 .664 .886 .59 -.175
15 170 192 69 109 101 83 167 174 71 124 98 65 0 0 67 108 15 81 92 46 84 27 184 163 1.217 .822 .663 1.144 1.242 3.083 120 625 3.853 .31 120 5150 10240 79 91 410 422 0 205 116 89 .878 186 69 1.139 .708 -.188 -.497
16 152 203 70 102 82 101 144 179 71 116 74 77 0 0 47 128 14 74 94 52 85 28 183 151 .812 1.232 1.041 1.41 1.506 3.058 156 819 4.624 .4 140 5340 10250 79 93 428 442 0 217 109 108 1.315 191 82 .76 1.111 .396 .152
17 129 171 77 102 52 69 123 144 79 116 46 42 0 0 48 116 19 76 65 34 53 21 121 88 .754 1.327 .913 1.903 1.916 5.745 32 176 9.629 .17 60 5520 10240 82 88 450 456 0 183 109 74 1.417 154 45 .706 .975 .503 -.036
18 128 166 70 101 58 65 131 158 75 119 61 57 0 0 38 104 26 80 78 37 56 12 123 118 .892 1.121 .934 1.32 1.457 2.777 32 176 4.216 .39 60 5720 10240 82 88 470 476 0 177 108 69 1.197 169 61 .835 .998 .259 -.003
19 138 212 82 106 56 106 135 235 93 133 53 129 0 0 28 92 35 97 75 58 33 16 162 182 .528 1.893 2.434 1.456 2.052 5.519 12 104 51.08 .04 50 2320 10490 107 112 130 135 0 226 113 113 2.022 251 138 .495 2.599 1.015 1.378
20 134 186 83 116 51 70 133 171 89 134 50 55 0 0 43 124 29 95 71 40 37 15 121 105 .729 1.373 1.1 1.744 1.867 3.6 32 176 13.597 .15 60 2550 10430 101 107 153 159 0 199 124 75 1.466 183 59 .682 1.175 .552 .232

Total number of rows: 4992

Table truncated, full table size 1057 Kbytes.




Supplementary data files not provided
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