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Sample GSM150398 Query DataSets for GSM150398
Status Public on Dec 15, 2006
Title NSH57 21-2 1wk: N3, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 21.1i; N3, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 21.1i; 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 21-2 1wk; N3, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 21-2 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 = 880, 8790; 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 = 32.03; Parameter Scan Time = 14:02:09; Parameter PMT Volts = 470; Parameter Scan Date = 2005-02-17; Parameter Pixel Size = 10; Parameter Laser on time = 58608; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.35; 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 = 32.03; Parameter Scan Time = 14:02:09; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-17; Parameter Pixel Size = 10; Parameter Laser on time = 58355; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.77; 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/2005-02/59529.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
1 214 90 106 58 108 32 145 69 107 66 39 11 0 0 492 145 22 37 58 25 45 10 140 50 3.375 .296 .282 .644 .727 3.456 120 771 .147 .43 120 2090 9890 104 116 115 127 0 147 95 52 .485 113 18 2.062 .462 -1.044 -1.115
2 163 83 103 60 60 23 155 74 106 68 52 14 0 0 54 46 23 38 70 25 53 12 83 66 2.609 .383 .269 .659 .886 3.475 120 748 1.114 .17 130 2310 9910 105 118 136 149 0 136 98 38 .627 121 23 1.594 .441 -.673 -1.182
3 165 92 105 54 60 38 158 82 106 67 53 28 0 0 50 48 24 39 76 40 56 17 98 81 1.579 .633 .528 .734 .771 3.555 80 510 .925 .22 100 2510 9890 105 115 158 168 0 151 88 62 1.037 134 46 .965 .865 .052 -.21
4 195 109 104 58 91 51 193 104 105 66 89 46 0 0 53 54 21 35 91 55 78 31 142 135 1.784 .56 .517 .597 .61 3.221 120 649 .748 .35 120 2720 9910 106 118 178 190 0 178 95 83 .917 170 75 1.09 .846 -.125 -.241
5 183 93 106 58 77 35 176 83 108 66 70 25 0 0 52 61 21 34 88 41 70 18 112 95 2.2 .455 .357 .519 .479 3.493 120 649 .916 .27 130 2910 9920 106 119 196 209 0 152 95 57 .744 136 41 1.344 .585 -.427 -.775
6 308 211 104 58 204 153 310 188 106 66 206 130 0 0 107 114 22 36 97 86 94 71 357 336 1.333 .75 .631 .699 .672 2.572 120 733 .793 .66 130 3110 9910 105 118 216 229 0 345 95 250 1.227 308 213 .815 1.033 .296 .047
7 158 92 102 61 56 31 150 74 105 67 48 13 0 0 52 60 21 37 71 33 54 18 87 61 1.806 .554 .271 .677 .676 4.847 120 608 1.501 .28 120 3320 9910 106 118 238 250 0 151 100 51 .906 121 21 1.104 .443 -.142 -1.174
8 150 72 104 57 46 15 146 66 108 66 42 9 0 0 37 38 28 38 66 23 38 7 61 51 3.067 .326 .214 .554 .6 3.88 120 707 4.183 .09 120 3510 9910 106 118 257 269 0 118 93 25 .534 108 15 1.874 .351 -.906 -1.512
9 177 76 104 57 73 19 170 68 105 64 66 11 0 0 50 37 20 34 90 30 69 9 92 77 3.842 .26 .167 .528 .561 2.561 52 340 .288 .18 80 3710 9890 106 114 279 287 0 124 93 31 .426 111 18 2.348 .273 -1.231 -1.874
10 151 91 107 58 44 33 143 86 110 67 36 28 0 0 33 48 27 39 59 40 37 9 77 64 1.333 .75 .778 1.112 .849 3.517 32 236 1.118 .26 70 3880 9910 108 115 296 303 0 149 95 54 1.227 141 46 .815 1.273 .296 .348
11 147 79 103 60 44 19 142 72 105 67 39 12 0 0 40 42 22 37 69 25 47 9 63 51 2.316 .432 .308 .754 .849 3.741 120 775 4.95 .08 130 4110 9910 105 118 316 329 0 129 98 31 .707 118 20 1.415 .504 -.501 -.99
12 144 82 104 58 40 24 135 75 105 65 31 17 0 0 42 43 22 35 61 30 38 17 64 48 1.667 .6 .548 1.034 .861 4.376 80 517 1.684 .16 100 4320 9900 106 116 339 349 0 134 95 39 .982 123 28 1.018 .898 -.026 -.156
13 162 82 105 59 57 23 153 68 106 67 48 9 0 0 43 44 23 35 79 34 52 12 80 57 2.478 .404 .188 .645 .869 4.087 120 807 1.047 .11 130 4520 9910 105 118 357 370 0 134 97 38 .66 111 15 1.514 .307 -.599 -1.704
14 158 78 106 58 52 20 155 78 107 67 49 20 0 0 35 39 21 35 80 28 56 11 72 69 2.6 .385 .408 .752 .683 2.785 80 526 1.359 .21 110 4730 9900 105 116 379 390 0 128 95 33 .629 128 33 1.589 .668 -.668 -.582
15 145 86 105 60 40 26 145 83 110 68 40 23 0 0 36 43 34 36 55 30 17 16 66 63 1.538 .65 .575 .834 .923 3.314 80 507 2.393 .16 100 4900 9920 108 118 397 407 0 141 98 43 1.064 136 38 .94 .941 .089 -.088
16 167 90 102 60 65 30 165 83 105 67 63 23 0 0 46 43 23 35 81 40 64 15 95 86 2.167 .462 .365 .543 .62 4.359 120 773 .796 .22 130 5120 9910 105 118 417 430 0 147 98 49 .755 136 38 1.324 .598 -.405 -.743
17 149 81 100 60 49 21 144 76 102 66 44 16 0 0 44 48 21 32 66 25 51 16 70 60 2.333 .429 .364 .784 .842 3.814 80 558 1.617 .2 110 5310 9900 105 116 437 448 0 133 98 34 .701 124 26 1.426 .595 -.512 -.749
18 151 83 98 57 53 26 144 73 100 64 46 16 0 0 39 46 25 33 67 38 46 21 79 62 2.038 .491 .348 .771 .833 4.205 52 340 1.261 .23 80 5510 9900 107 115 459 467 0 136 93 43 .803 119 26 1.246 .569 -.317 -.813
19 163 71 107 60 56 11 164 61 110 67 57 1 0 0 37 36 26 37 77 23 56 5 67 58 5.091 .196 .018 .664 .55 3.369 80 488 .423 .03 100 2120 10120 128 138 119 129 0 116 98 18 .321 100 2 3.111 .029 -1.637 -5.122
20 169 88 105 60 64 28 164 75 108 66 59 15 0 0 45 50 25 35 78 34 57 15 92 74 2.286 .438 .254 .541 .528 3.978 120 630 .889 .24 130 2310 10110 125 138 136 149 0 144 98 46 .716 123 25 1.397 .416 -.482 -1.265

Total number of rows: 4992

Table truncated, full table size 1022 Kbytes.




Supplementary data files not provided
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