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Sample GSM150401 Query DataSets for GSM150401
Status Public on Dec 15, 2006
Title NSH57 9-3 1wk: N3, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 9.2i; N3, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 9.2i; 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 9-3 1wk; N3, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 9-3 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 = 1290, 8430; 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 = 36.31; Parameter Scan Time = 14:35:20; Parameter PMT Volts = 530; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49748; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.50; 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 = 36.31; Parameter Scan Time = 14:35:20; Parameter PMT Volts = 630; Parameter Scan Date = 2004-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 49674; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.95; 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/2004-08/54732.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
1 179 94 86 66 93 28 163 75 87 75 77 9 0 0 75 57 25 45 88 28 67 15 121 86 3.321 .301 .117 .364 .527 5.412 52 308 .076 .12 80 2610 9490 102 110 128 136 0 85 60 25 .272 68 8 3.673 .106 -1.877 -3.242
2 189 92 85 64 104 28 159 79 90 72 74 15 0 0 244 50 46 43 65 28 37 13 132 89 3.714 .269 .203 .488 .486 4.871 80 584 .067 .15 110 2830 9460 97 108 148 159 0 83 58 25 .243 71 14 4.108 .183 -2.038 -2.448
3 172 180 90 65 82 115 167 159 94 73 77 94 0 0 73 89 39 43 74 79 48 55 197 171 .713 1.402 1.221 1.302 1.389 2.833 156 778 1.842 .48 140 3030 9480 98 112 167 181 0 163 59 104 1.268 144 85 .789 1.104 .343 .143
4 160 98 91 69 69 29 148 79 97 74 57 10 0 0 66 60 51 41 53 36 27 17 98 67 2.379 .42 .175 .536 .68 5.047 80 468 .114 .1 100 3220 9450 97 107 188 198 0 89 62 26 .38 71 9 2.631 .159 -1.396 -2.656
5 166 113 93 64 73 49 154 110 106 73 61 46 0 0 78 59 163 40 7 51 1 24 122 107 1.49 .671 .754 .743 .845 4.228 156 829 .371 .23 140 3430 9460 96 110 207 221 0 102 58 44 .607 99 42 1.648 .682 -.72 -.552
6 156 93 93 67 63 26 146 80 95 76 53 13 0 0 50 49 25 43 77 36 51 10 89 66 2.423 .413 .245 .71 .868 3.633 120 608 -1 -1 120 3640 9460 97 109 229 241 0 84 61 24 .373 72 12 2.68 .222 -1.422 -2.173
7 158 103 91 66 67 37 146 90 94 76 55 24 0 0 61 56 31 45 69 34 47 19 104 79 1.811 .552 .436 .797 .761 3.457 120 675 .799 .22 130 3830 9470 97 110 247 260 0 93 60 33 .499 81 22 2.003 .395 -1.002 -1.342
8 245 138 89 62 156 76 179 130 93 74 90 68 0 0 680 66 53 53 76 57 37 31 232 158 2.053 .487 .756 .783 .87 2.829 156 804 .021 .12 140 4040 9470 97 111 268 282 0 125 56 69 .441 118 61 2.27 .683 -1.183 -.55
9 163 93 88 66 75 27 146 80 94 75 58 14 0 0 69 58 69 62 40 23 13 5 102 72 2.778 .36 .241 .524 .483 4.094 52 359 .712 .7 90 4200 9450 97 106 286 295 0 84 60 24 .326 72 13 3.072 .218 -1.619 -2.196
10 174 108 91 68 83 40 142 93 92 74 51 25 0 0 223 67 24 42 70 39 50 22 123 76 2.075 .482 .49 .736 .72 4.132 120 683 .06 .11 120 4430 9460 97 109 308 320 0 98 61 36 .436 84 23 2.295 .443 -1.198 -1.174
11 204 123 91 65 113 58 153 110 92 73 62 45 0 0 367 64 24 44 78 50 60 25 171 107 1.948 .513 .726 .811 .782 3.579 156 772 .049 .16 140 4640 9470 97 111 328 342 0 111 59 52 .464 99 41 2.155 .656 -1.107 -.608
12 215 104 89 64 126 40 164 93 90 74 75 29 0 0 312 55 23 45 87 39 71 16 166 104 3.15 .317 .387 .639 .731 4.248 120 658 .043 .13 130 4830 9460 96 109 347 360 0 94 58 36 .287 84 26 3.484 .35 -1.801 -1.516
13 294 628 88 65 206 563 284 617 88 74 196 552 0 0 87 216 23 42 99 100 99 98 769 748 .366 2.733 2.816 2.776 2.8 1.616 156 862 2.917 .86 150 5040 9460 95 110 367 382 0 568 59 509 2.471 558 499 .405 2.547 1.305 1.349
14 225 328 88 69 137 259 218 316 89 75 130 247 0 0 68 130 24 42 97 96 93 90 396 377 .529 1.891 1.9 1.846 1.856 2.217 156 733 2.184 .7 140 5240 9460 96 110 388 402 0 297 62 234 1.709 286 223 .585 1.718 .774 .781
15 195 178 89 69 106 109 191 165 89 75 102 96 0 0 66 92 24 42 92 75 77 54 215 198 .972 1.028 .941 1.035 1.05 2.625 120 654 1.524 .55 130 5440 9460 96 109 408 421 0 161 62 99 .93 149 87 1.075 .851 -.105 -.233
16 270 399 90 69 180 330 258 385 93 75 168 316 0 0 93 171 27 41 98 100 95 97 510 484 .545 1.833 1.881 1.794 1.878 1.973 156 903 2.208 .77 150 5640 9470 96 111 427 442 0 361 62 298 1.658 348 286 .603 1.701 .729 .766
17 284 126 95 69 189 57 153 103 121 76 58 34 0 0 903 80 407 43 1 48 1 30 246 92 3.316 .302 .586 .986 1.054 3.73 52 408 .016 .1 90 5840 9440 96 105 450 459 0 114 62 52 .273 93 31 3.667 .53 -1.875 -.916
18 248 122 87 63 161 59 203 106 123 73 116 43 0 0 220 61 418 43 6 50 3 28 220 159 2.729 .366 .371 .437 .653 4.06 32 236 -.005 -.04 70 6020 9420 95 102 469 476 0 110 57 53 .331 96 39 3.018 .335 -1.593 -1.577
19 168 86 88 65 80 21 163 76 92 73 75 11 0 0 58 51 38 43 73 25 48 10 101 86 3.81 .263 .147 .489 .431 4.094 156 828 .253 .09 140 2640 9660 116 130 128 142 0 78 59 19 .237 69 10 4.213 .133 -2.075 -2.915
20 203 142 86 65 117 77 178 118 90 73 92 53 0 0 146 114 48 42 80 56 45 30 194 145 1.519 .658 .576 .74 .761 2.956 120 619 .605 .5 130 2850 9670 117 130 149 162 0 128 59 70 .595 107 48 1.68 .521 -.749 -.941

Total number of rows: 4992

Table truncated, full table size 1022 Kbytes.




Supplementary data files not provided
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