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Sample GSM150404 Query DataSets for GSM150404
Status Public on Dec 15, 2006
Title NSH57 9-4 1wk: S, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 9.2i; S, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 9.2i; 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 9-4 1wk; S, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 9-4 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 = 1530, 34780; 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 = 36.58; Parameter Scan Time = 14:47:06; Parameter PMT Volts = 480; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49757; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.48; 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 = 36.58; Parameter Scan Time = 14:47:06; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49683; 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/2004-08/54735.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 82 129 61 84 21 45 69 115 67 97 8 31 0 0 39 100 23 59 28 25 18 18 66 39 .467 2.143 3.875 3.713 2.444 4.89 32 176 13.52 .14 60 2750 35950 114 120 119 125 0 254 165 89 4.221 227 61 .237 7.633 2.078 2.932
2 141 113 63 89 78 24 139 106 67 104 76 17 0 0 53 66 18 71 81 18 75 6 102 93 3.25 .308 .224 .736 .702 4.999 32 236 -1 -1 70 2930 35950 113 120 136 143 0 223 175 47 .606 209 33 1.65 .441 -.722 -1.182
3 101 132 63 85 38 47 90 102 68 101 27 17 0 0 56 128 21 64 61 30 26 17 85 44 .809 1.237 .63 2.256 3.119 6.027 52 411 18.993 .08 90 3110 36000 117 126 153 162 0 260 167 93 2.436 201 33 .41 1.24 1.285 .311
4 125 130 67 92 58 38 119 125 75 107 52 33 0 0 43 68 28 67 66 33 50 8 96 85 1.526 .655 .635 .913 1.01 2.202 12 104 4.663 .24 50 3330 35940 113 118 177 182 0 256 181 75 1.291 246 65 .775 1.25 .368 .322
5 123 135 62 90 61 45 114 114 63 101 52 24 0 0 44 99 13 63 91 33 78 17 106 76 1.356 .738 .462 1.689 1.815 2.781 80 518 6.528 .18 100 3500 35980 115 125 192 202 0 266 177 89 1.453 225 47 .688 .909 .539 -.137
6 191 134 60 89 131 45 149 118 64 105 89 29 0 0 102 78 17 68 100 25 90 12 176 118 2.911 .344 .326 .406 .471 3.844 32 236 1.079 .21 70 3710 35950 113 120 214 221 0 264 175 89 .677 232 57 1.478 .642 -.564 -.64
7 218 135 62 88 156 47 184 110 63 102 122 22 0 0 141 80 12 67 90 36 81 15 203 144 3.319 .301 .18 .536 .565 5.191 80 515 .22 .13 100 3890 35960 113 123 231 241 0 266 173 93 .593 217 43 1.685 .355 -.753 -1.493
8 126 140 68 90 58 50 129 119 82 106 61 29 0 0 38 94 39 73 76 30 25 17 108 90 1.16 .862 .475 .925 1.273 4.524 52 334 11.413 .1 80 4070 35970 115 123 250 258 0 276 177 98 1.698 234 57 .589 .936 .764 -.095
9 263 171 63 87 200 84 242 160 65 99 179 73 0 0 155 113 14 61 92 55 86 28 284 252 2.381 .42 .408 .584 .618 5.042 52 340 .292 .25 80 4290 35950 113 121 272 280 0 337 171 165 .827 315 144 1.209 .803 -.274 -.316
10 173 155 62 93 111 62 128 128 65 106 66 35 0 0 104 100 23 66 82 38 61 25 173 101 1.79 .559 .53 1.33 1.205 6.904 52 340 .532 .14 80 4480 35950 113 121 291 299 0 305 183 122 1.1 252 69 .909 1.045 .138 .063
11 124 115 64 95 60 20 113 103 72 105 49 8 0 0 45 61 27 66 71 25 44 7 80 57 3 .333 .163 .884 .772 5.087 52 340 -24.625 -.04 80 4720 35940 112 120 315 323 0 227 187 39 .657 203 16 1.523 .322 -.607 -1.637
12 123 147 62 89 61 58 109 112 66 103 47 23 0 0 55 113 18 67 67 36 55 15 119 70 1.052 .951 .489 1.125 1.77 5.735 52 415 7.757 .2 90 4900 35960 113 122 332 341 0 290 175 114 1.873 221 45 .534 .964 .905 -.053
13 137 152 62 92 75 60 134 138 64 104 72 46 0 0 31 94 17 65 97 39 90 21 135 118 1.25 .8 .639 .919 1.084 3.49 120 735 7.89 .19 130 5110 35980 113 126 351 364 0 299 181 118 1.576 272 91 .635 1.258 .656 .332
14 95 114 61 88 34 26 92 100 64 101 31 12 0 0 29 67 16 64 70 28 48 7 60 43 1.308 .765 .387 1.385 1.515 4.758 156 972 21.441 .1 150 5300 35950 109 124 369 384 -50 225 173 51 1.506 197 24 .664 .762 .591 -.391
15 125 144 62 90 63 54 122 126 65 105 60 36 0 0 36 74 18 65 90 36 75 16 117 96 1.167 .857 .6 .913 1.189 3.815 80 559 4.728 .27 110 5540 35970 113 124 395 406 0 284 177 106 1.688 248 71 .592 1.182 .756 .241
16 123 139 60 87 63 52 121 120 63 101 61 33 0 0 31 83 16 63 97 35 86 18 115 94 1.212 .825 .541 .859 .896 3.069 80 552 8.199 .21 110 5720 35960 112 123 413 424 0 274 171 102 1.626 236 65 .615 1.066 .701 .092
17 93 158 71 92 22 66 87 149 80 103 16 57 0 0 38 78 30 65 33 50 25 25 88 73 .333 3 3.563 1.239 1.348 4.668 12 104 10.613 .16 50 5860 35940 113 118 430 435 0 311 181 130 5.909 293 112 .169 7.017 2.563 2.811
18 80 102 61 91 19 11 69 95 63 101 8 4 0 0 29 62 15 62 39 14 28 5 30 12 1.727 .579 .5 2.512 2.769 5.194 156 1090 43.727 .05 150 6100 35950 109 124 449 464 -50 201 179 22 1.14 187 8 .877 .985 .19 -.022
19 86 108 62 87 24 21 82 93 64 100 20 6 0 0 29 73 16 66 57 21 33 7 45 26 1.143 .875 .3 2.195 2.143 4.059 156 1045 -1 -1 150 2710 36160 130 145 110 125 -50 213 171 41 1.724 183 12 .58 .591 .785 -.759
20 105 159 65 92 40 67 103 119 67 105 38 27 0 0 28 272 17 70 76 33 55 7 107 65 .597 1.675 .711 2.374 2.377 3.143 80 507 33.489 .14 110 2910 36200 136 147 132 143 0 313 181 132 3.299 234 53 .303 1.4 1.722 .485

Total number of rows: 4992

Table truncated, full table size 1044 Kbytes.




Supplementary data files not provided
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