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Sample GSM150496 Query DataSets for GSM150496
Status Public on Dec 15, 2006
Title NSH57 14-2 1wk: N3, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 14.1i; N3, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 14.1i; 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 14-2 1wk; N3, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 14-2 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 = 840, 35430; 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 = 31.85; Parameter Scan Time = 11:15:47; Parameter PMT Volts = 510; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 49393; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.47; 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 = 31.85; Parameter Scan Time = 11:15:47; Parameter PMT Volts = 640; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 49319; 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/2004-08/54693.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
1 166 93 75 70 91 23 170 99 76 78 95 29 0 0 57 43 21 48 90 34 75 3 114 124 3.957 .253 .305 .568 .48 3.51 32 176 1.166 .13 60 2250 36780 132 138 138 144 0 109 82 27 .295 116 34 3.389 .356 -1.761 -1.489
2 170 89 86 65 84 24 162 103 95 76 76 38 0 0 56 43 36 46 83 41 58 0 108 114 3.5 .286 .5 .81 .638 1.681 12 104 1.346 .15 50 2430 36760 130 135 156 161 0 104 76 28 .334 120 44 2.998 .584 -1.584 -.777
3 175 108 82 64 93 44 172 110 85 77 90 46 0 0 50 56 27 49 90 46 78 18 137 136 2.114 .473 .511 .843 .702 2.992 32 236 1.053 .25 70 2650 36730 126 133 177 184 0 126 75 51 .552 128 54 1.81 .597 -.856 -.745
4 138 94 85 66 53 28 133 89 90 77 48 23 0 0 45 47 28 46 62 40 43 9 81 71 1.893 .528 .479 1.261 1.298 3.459 32 236 3.396 .11 70 2850 36750 128 135 197 204 0 110 77 33 .617 104 27 1.621 .559 -.697 -.838
5 145 102 83 67 62 35 132 90 86 73 49 23 0 0 54 52 24 45 82 34 50 19 97 72 1.771 .565 .469 .691 1 4.736 52 420 6.355 .06 90 3040 36730 125 134 215 224 0 119 78 41 .659 105 27 1.517 .548 -.602 -.868
6 146 81 86 62 60 19 149 72 91 69 63 10 0 0 50 49 29 40 71 25 53 9 79 73 3.158 .317 .159 .697 .528 3.323 32 176 .791 .14 60 3250 36740 128 134 238 244 0 95 72 22 .37 84 12 2.705 .185 -1.436 -2.432
7 137 89 80 62 57 27 133 80 82 72 53 18 0 0 54 62 23 44 71 30 59 15 84 71 2.111 .474 .34 .655 .593 4.796 52 336 6.166 .03 80 3440 36760 129 137 256 264 0 104 72 32 .553 93 21 1.808 .396 -.855 -1.335
8 150 101 82 64 68 37 149 89 97 75 67 25 0 0 56 62 291 46 0 31 0 16 105 92 1.838 .544 .373 .785 .735 3.404 120 641 .01 .07 120 3670 36750 126 138 277 289 0 118 75 43 .635 104 29 1.574 .436 -.655 -1.199
9 86 74 84 66 2 8 83 65 95 75 -1 -1 0 0 24 44 248 45 0 17 0 5 10 -2 .25 4 null 2.01 2.091 3.918 156 882 .004 .06 150 3850 36740 123 138 293 308 -50 86 77 9 4.67 76 -1 .214 null 2.223 null
10 180 99 80 64 100 35 186 79 83 72 106 15 0 0 67 66 29 43 84 37 65 18 135 121 2.857 .35 .142 .611 .684 3.599 32 236 .339 .2 70 4040 36740 127 134 316 323 0 116 75 41 .409 92 18 2.447 .165 -1.291 -2.598
11 129 88 82 70 47 18 129 85 87 79 47 15 0 0 39 52 24 46 69 23 48 7 65 62 2.611 .383 .319 .814 .802 4.102 52 340 8.156 .09 80 4260 36730 126 134 338 346 0 103 82 21 .447 99 18 2.237 .373 -1.161 -1.424
12 138 106 82 67 56 39 124 88 84 76 42 21 0 0 59 73 23 47 65 30 48 17 95 63 1.436 .696 .5 1.029 1.328 3.478 52 420 2.924 .25 90 4450 36730 125 134 356 365 0 124 78 46 .813 103 25 1.23 .584 -.299 -.777
13 169 135 78 63 91 72 172 120 80 72 94 57 0 0 50 79 21 45 92 56 81 37 163 151 1.264 .791 .606 .883 .954 2.959 120 848 2.124 .37 130 4680 36740 124 137 377 390 0 158 74 84 .924 140 67 1.083 .708 -.115 -.498
14 142 91 81 64 61 27 135 84 83 74 54 20 0 0 39 53 22 46 85 35 63 10 88 74 2.259 .443 .37 .827 .96 3.522 80 486 6.379 .05 100 4870 36730 125 135 398 408 0 106 75 32 .517 98 23 1.935 .432 -.952 -1.21
15 1545 183 80 63 1465 120 1621 164 84 72 1541 101 0 0 567 96 24 45 100 73 100 53 1585 1642 12.208 .082 .066 .066 .079 3.103 120 745 .073 .62 130 5080 36740 124 137 417 430 0 214 74 140 .096 191 118 10.457 .077 -3.386 -3.708
16 157 124 78 63 79 61 155 110 80 71 77 47 0 0 52 73 23 42 85 54 73 30 140 124 1.295 .772 .61 .758 .863 3.405 156 922 1.748 .3 150 5290 36750 124 139 437 452 0 145 74 71 .901 128 55 1.109 .713 -.15 -.489
17 219 149 76 66 143 83 202 124 76 72 126 58 0 0 104 96 20 42 88 65 78 42 226 184 1.723 .58 .46 .709 .666 3.838 52 289 .623 .47 80 5450 36750 128 136 457 465 0 174 77 97 .678 145 68 1.476 .537 -.561 -.896
18 233 114 74 64 159 50 232 103 75 75 158 39 0 0 102 64 21 46 90 40 84 18 209 197 3.18 .314 .247 .349 .376 2.981 32 176 .291 .32 60 5650 36740 128 134 478 484 0 133 75 58 .367 120 46 2.724 .288 -1.446 -1.795
19 157 95 88 63 69 32 149 80 96 73 61 17 0 0 49 59 39 45 66 33 33 16 101 78 2.156 .464 .279 .558 .606 3.189 12 104 1.443 .23 50 2230 36950 149 154 136 141 0 111 74 37 .541 93 20 1.847 .325 -.885 -1.62
20 136 87 75 62 61 25 131 80 78 72 56 18 0 0 49 52 24 46 67 30 58 15 86 74 2.44 .41 .321 .793 .888 4.049 80 586 2.271 .12 110 2460 36950 146 157 156 167 0 102 72 29 .478 93 21 2.09 .375 -1.064 -1.414

Total number of rows: 4992

Table truncated, full table size 1027 Kbytes.




Supplementary data files not provided
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