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Sample GSM150606 Query DataSets for GSM150606
Status Public on Dec 15, 2006
Title NSH79 14-4 1wk: N3, 2C
Sample type genomic
 
Channel 1
Source name NSH79 14 input 2 N3, 2C
Organism Helicobacter pylori
Characteristics NSH79 14 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 NSH79 14-4 1wk; N3, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH79 14-4 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 = 940, 35220; 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 = 31.88; Parameter Scan Time = 12:38:40; Parameter PMT Volts = 480; Parameter Scan Date = 2004-03-23; Parameter Pixel Size = 10; Parameter Laser on time = 43367; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.38; 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 = 31.88; Parameter Scan Time = 12:38:40; Parameter PMT Volts = 460; Parameter Scan Date = 2004-03-23; Parameter Pixel Size = 10; Parameter Laser on time = 43375; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.82; 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/2004-03/50520.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)
GSE6529 NSH79 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
1 153 66 57 33 96 33 143 64 59 35 86 31 0 0 48 19 16 12 95 83 92 62 129 117 2.909 .344 .36 .335 .346 1.923 80 568 .259 .67 110 1830 36240 96 107 83 94 0 161 81 81 .84 156 76 1.19 .881 -.251 -.183
2 131 61 57 34 74 27 127 58 58 35 70 24 0 0 47 20 15 8 89 80 84 60 101 94 2.741 .365 .343 .331 .35 2.282 120 641 .318 .69 120 2040 36240 96 108 104 116 0 149 83 66 .892 142 59 1.121 .838 -.165 -.255
3 151 96 57 34 94 62 153 94 59 35 96 60 0 0 43 36 17 6 97 97 90 95 156 156 1.516 .66 .625 .616 .649 1.946 120 696 .615 .8 130 2240 36230 94 107 123 136 0 235 83 152 1.612 230 147 .62 1.528 .689 .611
4 130 89 58 34 72 55 137 89 60 35 79 55 0 0 41 29 19 10 84 96 75 86 127 134 1.309 .764 .696 .829 .741 2.487 120 696 .624 .7 130 2440 36220 93 106 143 156 0 218 83 134 1.867 218 134 .536 1.702 .901 .767
5 141 117 56 34 85 83 137 114 58 36 81 80 0 0 45 38 14 21 94 98 90 85 168 161 1.024 .976 .988 1 1.007 2.079 120 658 1.056 .72 120 2640 36230 95 107 164 176 0 286 83 203 2.387 279 196 .419 2.414 1.255 1.272
6 121 54 57 34 64 20 119 49 58 36 62 15 0 0 45 20 14 19 82 43 75 18 84 77 3.2 .313 .242 .284 .3 2.746 120 637 .424 .45 120 2850 36220 94 106 185 197 0 132 83 49 .764 120 37 1.309 .591 -.389 -.758
7 169 69 58 34 111 35 151 65 59 35 93 31 0 0 75 26 14 7 95 90 90 82 146 124 3.171 .315 .333 .327 .294 2.092 120 579 .25 .71 120 3040 36230 95 107 204 216 0 169 83 86 .771 159 76 1.297 .815 -.376 -.295
8 431 89 58 35 373 54 416 85 62 36 358 50 0 0 101 24 22 8 100 99 100 97 427 408 6.907 .145 .14 .137 .139 1.605 120 793 .135 .85 130 3240 36220 93 106 223 236 0 218 86 132 .354 208 122 2.826 .341 -1.499 -1.55
9 211 64 58 35 153 29 180 53 60 37 122 18 0 0 229 32 15 8 96 76 92 50 182 140 5.276 .19 .148 .186 .18 2.519 52 396 .118 .71 90 3450 36240 97 106 246 255 0 156 86 71 .463 130 44 2.158 .361 -1.11 -1.471
10 138 65 58 36 80 29 130 56 60 37 72 20 0 0 71 50 15 8 92 77 86 61 109 92 2.759 .363 .278 .332 .333 2.812 80 531 .294 .54 110 3650 36220 94 105 265 276 0 159 88 71 .886 137 49 1.128 .679 -.174 -.558
11 142 62 58 36 84 26 128 58 61 37 70 22 0 0 82 22 20 15 87 64 77 33 110 92 3.231 .31 .314 .317 .356 2.76 156 866 .222 .46 150 3840 36220 92 107 282 297 0 152 88 64 .757 142 54 1.322 .768 -.402 -.38
12 143 66 59 36 84 30 132 61 61 37 73 25 0 0 61 28 17 8 95 80 88 67 114 98 2.8 .357 .342 .337 .327 2.823 120 590 .271 .59 120 4040 36220 94 106 304 316 0 161 88 73 .873 149 61 1.145 .837 -.196 -.256
13 134 63 59 36 75 27 138 59 61 37 79 23 0 0 38 22 15 8 92 82 88 66 102 102 2.778 .36 .291 .305 .31 2.34 156 854 .3 .61 140 4240 36210 92 106 323 337 0 154 88 66 .88 144 56 1.136 .712 -.184 -.491
14 135 58 59 36 76 22 133 55 60 37 74 19 0 0 44 17 18 20 92 48 82 11 98 93 3.455 .289 .257 .284 .285 2.413 156 736 .239 .57 140 4440 36220 93 107 343 357 0 142 88 54 .708 134 46 1.413 .628 -.499 -.672
15 422 98 59 35 363 63 435 98 61 36 376 63 0 0 126 30 21 10 100 99 100 94 426 439 5.762 .174 .168 .164 .165 1.644 120 658 .153 .82 130 4630 36210 92 105 362 375 0 240 86 154 .424 240 154 2.357 .41 -1.237 -1.288
16 129 87 58 35 71 52 127 87 60 36 69 52 0 0 38 25 21 9 91 94 78 89 123 121 1.365 .732 .754 .788 .698 2.62 156 867 .617 .74 140 4840 36200 91 105 383 397 0 213 86 127 1.79 213 127 .559 1.842 .84 .881
17 135 60 57 37 78 23 135 56 60 38 78 19 0 0 45 18 21 9 90 71 73 53 101 97 3.391 .295 .244 .23 .291 2.882 52 414 .239 .69 90 5050 36200 93 102 406 415 0 147 90 56 .721 137 46 1.387 .595 -.472 -.748
18 146 185 59 37 87 148 149 172 60 39 90 135 0 0 47 61 15 11 92 100 87 100 235 225 .588 1.701 1.5 1.861 1.701 2.2 80 554 1.643 .77 100 5250 36210 94 104 426 436 0 452 90 362 4.158 420 330 .24 3.667 2.056 1.875
19 146 77 60 34 86 43 146 76 67 36 86 42 0 0 47 23 66 19 67 85 15 55 129 128 2 .5 .488 .502 .492 2.309 156 782 .426 .8 140 1840 36430 114 128 83 97 0 188 83 105 1.222 186 103 .818 1.194 .29 .256
20 150 49 59 34 91 15 150 47 61 34 91 13 0 0 34 13 13 7 100 71 98 44 106 104 6.067 .165 .143 .151 .167 2.183 120 526 .156 .62 120 2040 36430 115 127 104 116 0 120 83 37 .403 115 32 2.482 .349 -1.311 -1.518

Total number of rows: 4992

Table truncated, full table size 1003 Kbytes.




Supplementary data files not provided
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