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Sample GSM150457 Query DataSets for GSM150457
Status Public on Dec 15, 2006
Title NSH57 2-1 1wk: N3, 2C
Sample type genomic
 
Channel 1
Source name NSH57 1 input 2 N3, 2C
Organism Helicobacter pylori
Characteristics NSH57 1 input 2 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 2-1 1wk; N3, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 2-1 1wk; 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 = 1840, 9080; 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 = 32.00; Parameter Scan Time = 15:33:03; Parameter PMT Volts = 440; Parameter Scan Date = 2004-05-06; Parameter Pixel Size = 10; Parameter Laser on time = 45584; 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 = 32.00; Parameter Scan Time = 15:33:03; Parameter PMT Volts = 520; Parameter Scan Date = 2004-05-06; Parameter Pixel Size = 10; Parameter Laser on time = 45592; 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/2004-05/51918.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
1 131 112 43 35 88 77 133 107 43 37 90 72 0 0 37 48 8 11 97 93 96 87 165 162 1.143 .875 .8 .764 .803 2.258 156 984 .957 .75 150 2680 10000 84 99 76 91 0 142 44 98 1.112 136 91 .899 1.017 .153 .024
2 135 116 43 35 92 81 139 112 44 37 96 77 0 0 38 50 8 11 100 92 97 90 173 173 1.136 .88 .802 .824 .806 1.831 120 628 .969 .79 130 2880 10010 86 99 97 110 0 147 44 103 1.119 142 98 .894 1.019 .162 .027
3 162 162 43 34 119 128 158 151 44 36 115 117 0 0 49 68 8 10 100 100 100 99 247 232 .93 1.076 1.017 1.011 1.049 1.698 120 653 1.123 .82 130 3080 10000 85 98 117 130 0 206 43 163 1.367 192 149 .732 1.293 .451 .371
4 175 114 44 35 131 79 171 104 44 37 127 69 0 0 80 56 8 11 98 91 97 82 210 196 1.658 .603 .543 .542 .571 2.33 156 734 .559 .74 140 3290 10000 85 99 138 152 0 145 44 100 .766 132 88 1.305 .69 -.384 -.535
5 210 186 44 36 166 150 208 178 45 38 164 142 0 0 101 80 8 12 95 98 94 96 316 306 1.107 .904 .866 .986 .91 2.629 156 711 .846 .86 140 3490 9990 84 98 158 172 0 236 46 191 1.148 226 180 .871 1.1 .199 .138
6 210 112 44 36 166 76 163 99 45 37 119 63 0 0 132 69 8 12 99 79 98 67 242 182 2.184 .458 .529 .46 .48 2.802 156 704 .417 .77 140 3690 10000 85 99 178 192 0 142 46 97 .582 126 80 1.719 .673 -.781 -.572
7 200 143 45 35 155 108 142 106 46 38 97 71 0 0 135 105 9 11 98 90 93 80 263 168 1.435 .697 .732 .669 .715 2.612 120 659 .681 .76 130 3900 9990 84 97 199 212 0 182 44 137 .885 135 90 1.129 .93 -.176 -.105
8 1843 3713 46 39 1797 3674 1971 3904 47 41 1925 3865 0 0 451 997 10 14 100 100 100 100 5471 5790 .489 2.045 2.008 2.006 2.048 1.726 156 820 2.123 .94 140 4100 9990 84 98 219 233 0 4718 50 4669 2.598 4961 4911 .385 2.551 1.377 1.351
9 288 386 47 39 241 347 211 279 49 42 164 240 0 0 205 296 18 15 96 96 92 96 588 404 .695 1.44 1.463 1.383 1.267 2.432 80 520 1.503 .76 110 4310 9980 84 95 241 252 0 490 50 441 1.83 355 305 .547 1.86 .872 .895
10 157 145 45 36 112 109 129 117 47 38 84 81 0 0 94 94 12 10 95 87 87 82 221 165 1.028 .973 .964 .867 .996 2.755 120 690 .947 .75 130 4490 9980 83 96 258 271 0 184 46 139 1.237 149 103 .809 1.225 .306 .293
11 282 215 45 36 237 179 280 211 46 38 235 175 0 0 70 69 10 11 100 100 100 100 416 410 1.324 .755 .745 .733 .727 1.528 120 692 .727 .87 130 4690 9980 83 96 278 291 0 273 46 227 .96 268 222 1.042 .946 -.059 -.08
12 166 97 45 36 121 61 149 83 46 38 104 47 0 0 64 53 14 12 98 86 96 75 182 151 1.984 .504 .452 .42 .425 2.665 156 722 .526 .7 140 4900 9990 84 98 299 313 0 123 46 78 .641 105 60 1.561 .574 -.642 -.8
13 141 86 45 36 96 50 143 84 45 38 98 48 0 0 31 24 9 11 99 97 97 87 146 146 1.92 .521 .49 .51 .523 2.037 156 743 .469 .73 140 5090 9980 83 97 318 332 0 109 46 64 .662 107 61 1.511 .622 -.595 -.684
14 106 116 46 36 60 80 104 116 47 39 58 80 0 0 25 37 10 12 98 97 96 92 140 138 .75 1.333 1.379 1.324 1.308 1.9 156 748 1.474 .75 140 5300 9990 84 98 339 353 0 147 46 102 1.694 147 102 .59 1.753 .761 .81
15 18275 2243 48 37 18227 2206 18293 2332 51 40 18245 2295 0 0 4267 696 13 13 100 98 100 97 20433 20540 8.262 .121 .126 .11 .122 1.986 156 722 .117 .94 140 5500 9990 84 98 359 373 0 2850 47 2803 .154 2963 2916 6.502 .16 -2.701 -2.645
16 201 107 49 37 152 70 207 103 51 40 158 66 0 0 50 34 12 13 99 96 99 93 222 224 2.171 .461 .418 .435 .441 1.996 156 804 .426 .78 140 5700 9980 83 97 379 393 0 136 47 89 .585 131 84 1.709 .531 -.773 -.914
17 391 128 46 37 345 91 299 101 48 38 253 64 0 0 321 86 11 11 100 85 96 74 436 317 3.791 .264 .253 .254 .281 2.829 120 676 .218 .78 130 5900 9980 83 96 399 412 0 163 47 116 .335 128 81 2.984 .321 -1.577 -1.637
18 218 103 45 36 173 67 191 77 46 38 146 41 0 0 135 73 10 11 99 75 98 65 240 187 2.582 .387 .281 .337 .368 3.234 120 774 .352 .68 130 6110 9980 83 96 420 433 0 131 46 85 .492 98 52 2.032 .357 -1.023 -1.487
19 92 51 43 35 49 16 93 48 44 37 50 13 0 0 18 23 8 11 98 53 96 28 65 63 3.063 .327 .26 .319 .356 2.958 156 699 .424 .44 140 2700 10200 105 119 79 93 0 65 44 20 .415 61 17 2.41 .33 -1.269 -1.598
20 83 43 43 34 40 9 82 40 44 37 39 6 0 0 19 13 8 10 94 38 90 18 49 45 4.444 .225 .154 .278 .354 2.919 156 526 .168 .24 140 2900 10200 105 119 99 113 0 55 43 11 .286 51 8 3.498 .195 -1.806 -2.355

Total number of rows: 4992

Table truncated, full table size 1014 Kbytes.




Supplementary data files not provided
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