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Sample GSM150520 Query DataSets for GSM150520
Status Public on Dec 15, 2006
Title NSH57 1-2 1wk: S, 2C
Sample type genomic
 
Channel 1
Source name NSH57 1 input 2 S, 2C
Organism Helicobacter pylori
Characteristics NSH57 1 input 2 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 1-2 1wk; S, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 1-2 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 = 1770, 35670; 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 = 31.30; Parameter Scan Time = 11:52:49; Parameter PMT Volts = 400; Parameter Scan Date = 2004-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 45619; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.44; 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 = 31.30; Parameter Scan Time = 11:52:49; Parameter PMT Volts = 480; Parameter Scan Date = 2004-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 45627; 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/2004-05/51934.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 41 43 39 39 2 4 40 40 39 40 1 1 0 0 8 18 6 10 18 23 8 9 6 2 .5 2 1 1.526 1.333 3.062 156 1023 4.591 .33 150 2690 36800 105 120 84 99 -50 39 36 4 1.834 37 1 .545 .917 .875 -.125
2 255 161 40 38 215 123 202 135 40 40 162 97 0 0 171 90 6 10 99 95 98 90 338 259 1.748 .572 .599 .612 .61 2.014 120 594 .509 .85 120 2900 36810 108 120 107 119 0 148 35 113 .525 124 89 1.906 .549 -.93 -.865
3 204 165 40 39 164 126 115 139 40 40 75 100 0 0 183 99 6 10 95 96 93 92 290 175 1.302 .768 1.333 1.054 1.002 2.71 120 717 .58 .84 130 3090 36800 106 119 125 138 0 151 36 116 .705 127 92 1.419 1.223 -.505 .29
4 348 206 41 39 307 167 292 170 42 41 251 131 0 0 259 131 7 11 99 93 99 90 474 382 1.838 .544 .522 .574 .569 2.106 120 636 .496 .9 120 3300 36800 107 119 147 159 0 189 36 153 .499 156 120 2.004 .479 -1.003 -1.063
5 267 210 42 38 225 172 161 169 43 41 119 131 0 0 223 137 9 11 99 97 95 94 397 250 1.308 .764 1.101 .885 .909 1.849 120 623 .658 .91 120 3500 36800 107 119 167 179 0 193 35 158 .701 155 120 1.426 1.01 -.512 .014
6 341 221 40 38 301 183 199 165 41 40 159 127 0 0 286 146 6 10 100 100 99 97 484 286 1.645 .608 .799 .716 .655 2.131 120 733 .515 .87 130 3700 36790 105 118 186 199 0 203 35 168 .558 151 116 1.793 .733 -.843 -.449
7 356 249 42 41 314 208 174 160 46 44 132 119 0 0 349 195 37 20 86 96 63 88 522 251 1.51 .662 .902 .827 .799 2.005 80 548 .562 .86 110 3900 36790 106 117 207 218 0 228 38 191 .608 147 109 1.646 .827 -.719 -.274
8 3877 2420 44 42 3833 2378 3950 2438 47 44 3906 2396 0 0 426 260 32 18 100 100 100 100 6211 6302 1.612 .62 .613 .621 .626 1.127 120 768 .606 .98 130 4100 36790 105 118 226 239 0 2220 39 2181 .569 2236 2198 1.757 .563 -.813 -.83
9 356 255 43 42 313 213 310 221 44 43 267 179 0 0 242 150 8 11 98 96 97 93 526 446 1.469 .681 .67 .7 .674 2.074 80 463 .621 .86 100 4310 36810 109 119 249 259 0 234 39 195 .624 203 164 1.602 .615 -.68 -.702
10 135 121 41 40 94 81 102 97 41 41 61 57 0 0 92 69 6 10 96 89 94 86 175 118 1.16 .862 .934 .851 .87 2.052 120 631 .77 .84 120 4500 36790 106 118 267 279 0 111 37 74 .79 89 52 1.265 .857 -.339 -.222
11 111 193 40 39 71 154 104 181 41 40 64 142 0 0 31 60 6 10 100 100 100 100 225 206 .461 2.169 2.219 2.206 2.266 1.482 120 696 2.308 .88 130 4700 36780 104 117 286 299 0 177 36 141 1.99 166 130 .503 2.035 .992 1.025
12 150 627 40 38 110 589 103 162 40 40 63 124 0 0 246 3585 5 10 100 99 99 99 699 187 .187 5.355 1.968 1.992 1.929 2.049 120 625 49.909 .27 120 4900 36790 106 118 307 319 0 575 35 540 4.911 149 114 .204 1.805 2.296 .852
13 85 83 40 38 45 45 84 82 40 40 44 44 0 0 13 22 5 10 100 97 100 85 90 88 1 1 1 .914 .975 1.805 120 675 1.225 .78 120 5100 36780 105 117 327 339 0 76 35 41 .917 75 40 1.09 .917 -.125 -.125
14 69 51 40 38 29 13 69 51 41 40 29 13 0 0 12 12 6 10 96 57 92 25 42 42 2.231 .448 .448 .493 .559 2.516 120 695 .635 .4 130 5300 36780 104 117 346 359 0 47 35 12 .411 47 12 2.432 .411 -1.282 -1.282
15 85 58 40 38 45 20 83 54 41 40 43 16 0 0 19 19 6 10 98 63 97 45 65 59 2.25 .444 .372 .38 .461 2.64 120 622 .504 .55 120 5500 36780 105 117 367 379 0 53 35 18 .408 50 15 2.453 .341 -1.295 -1.551
16 76 68 40 39 36 29 75 66 41 40 35 27 0 0 14 18 6 10 99 83 95 64 65 62 1.241 .806 .771 .746 .809 2.306 120 776 1.005 .66 130 5700 36780 104 117 386 399 0 62 36 27 .739 61 25 1.353 .708 -.437 -.499
17 137 142 42 39 95 103 122 129 44 42 80 90 0 0 65 71 16 16 90 92 80 84 198 170 .922 1.084 1.125 1.14 .966 1.936 52 334 1.168 .81 80 5890 36770 106 114 408 416 0 130 36 94 .994 118 83 1.006 1.032 -.008 .045
18 154 154 41 40 113 114 122 117 42 42 81 77 0 0 87 87 13 14 97 97 93 90 227 158 .991 1.009 .951 .989 .949 1.915 80 524 .959 .84 100 6100 36790 107 117 428 438 0 141 37 105 .925 107 71 1.081 .872 -.112 -.198
19 69 61 39 39 30 22 69 60 39 40 30 21 0 0 12 16 6 10 99 72 95 50 52 51 1.364 .733 .7 .639 .722 2.467 120 708 1.062 .54 130 2690 37000 126 139 85 98 0 56 36 20 .673 55 19 1.487 .642 -.572 -.639
20 67 58 39 39 28 19 64 57 40 40 25 18 0 0 9 17 6 10 100 65 96 40 47 43 1.474 .679 .72 .633 .7 2.5 120 618 1.173 .48 130 2900 37000 126 139 106 119 0 53 36 17 .622 52 17 1.607 .66 -.684 -.599

Total number of rows: 4992

Table truncated, full table size 999 Kbytes.




Supplementary data files not provided
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