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Sample GSM150394 Query DataSets for GSM150394
Status Public on Dec 15, 2006
Title NSH57 19-1 1wk: N3, 2C
Sample type genomic
 
Channel 1
Source name input mouse NSH57 19.1i; N3, 2C
Organism Helicobacter pylori
Characteristics input mouse NSH57 19.1i; 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 19-1 1wk; N3, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH57 19-1 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 = 640, 8400; 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 = 32.13; Parameter Scan Time = 13:49:38; Parameter PMT Volts = 430; Parameter Scan Date = 2005-02-17; Parameter Pixel Size = 10; Parameter Laser on time = 58595; 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 = 32.13; Parameter Scan Time = 13:49:38; Parameter PMT Volts = 590; Parameter Scan Date = 2005-02-17; Parameter Pixel Size = 10; Parameter Laser on time = 58343; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.76; 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/2005-02/59525.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 72 56 66 53 6 3 68 48 66 60 2 -5 0 0 18 30 11 30 23 15 13 5 9 -3 2 .5 null 2.416 2.461 3.567 156 942 -60.427 -.03 150 2030 9890 141 156 131 146 -50 57 54 3 .508 49 -5 1.969 null -.978 null
2 80 59 67 53 13 6 79 52 67 59 12 -1 0 0 21 30 11 30 50 17 33 6 19 11 2.167 .462 null 1.17 1.269 4.329 156 775 -1 -1 150 2230 9890 141 156 151 166 -50 60 54 6 .469 53 -1 2.133 null -1.093 null
3 82 60 69 53 13 7 81 52 69 59 12 -1 0 0 19 33 11 31 51 16 25 6 20 11 1.857 .538 null 1.235 1.108 3.678 156 840 -1 -1 150 2430 9890 141 156 171 186 -50 61 54 7 .547 53 -1 1.828 null -.871 null
4 84 60 69 55 15 5 81 53 69 61 12 -2 0 0 21 33 11 32 51 18 32 3 20 10 3 .333 null 1.57 1.643 4.088 156 810 -1 -1 150 2630 9890 141 156 191 206 -50 61 56 5 .339 54 -2 2.954 null -1.563 null
5 85 60 69 54 16 6 83 55 69 60 14 1 0 0 20 32 11 30 54 21 37 5 22 15 2.667 .375 .071 1.201 1.667 3.731 156 824 36.457 .04 150 2830 9890 141 156 211 226 -50 61 55 6 .381 56 1 2.626 .073 -1.393 -3.785
6 75 59 69 53 6 6 74 57 69 59 5 4 0 0 16 28 11 29 30 17 14 3 12 9 1 1 .8 1.773 2 4.115 156 801 -1 -1 150 3030 9880 140 155 231 246 -50 60 54 6 1.016 58 4 .985 .813 .022 -.299
7 80 59 68 53 12 6 78 50 69 59 10 -3 0 0 17 32 11 30 42 19 26 4 18 7 2 .5 null 1.841 2.158 3.772 156 774 27.262 .06 150 3230 9880 140 155 251 266 -50 60 54 6 .508 51 -3 1.969 null -.978 null
8 85 64 68 52 17 12 83 62 69 59 15 10 0 0 18 30 11 30 60 27 34 7 29 25 1.417 .706 .667 1.585 1.459 3.875 156 766 25.959 .05 150 3430 9880 140 155 271 286 -50 65 53 12 .717 63 10 1.395 .677 -.48 -.563
9 72 60 69 53 3 7 69 52 70 59 0 -1 0 0 17 30 11 29 24 20 12 7 10 -1 .429 2.333 null 2.299 2.215 4.549 156 788 -80.11 -.03 150 3630 9880 140 155 291 306 -50 61 54 7 2.37 53 -1 .422 null 1.245 null
10 81 63 69 55 12 8 80 56 70 61 11 1 0 0 17 31 11 30 48 22 24 8 20 12 1.5 .667 .091 1.511 1.757 4.186 156 860 -1 -1 150 3830 9880 140 155 311 326 -50 64 56 8 .677 57 1 1.477 .092 -.563 -3.437
11 81 57 68 56 13 1 78 53 69 61 10 -3 0 0 18 29 11 30 45 14 26 3 14 7 13 .077 null 1.758 2.117 4.256 156 810 39.234 .03 150 4030 9880 140 155 331 346 -50 58 57 1 .078 54 -3 12.799 null -3.678 null
12 82 62 69 54 13 8 80 54 70 60 11 0 0 0 18 34 11 30 48 21 29 8 21 11 1.625 .615 null 1.51 1.802 4.631 156 914 -1 -1 150 4230 9880 140 155 351 366 -50 63 55 8 .625 55 0 1.6 null -.678 null
13 80 62 69 55 11 7 79 57 69 61 10 2 0 0 16 32 12 31 43 19 17 6 18 12 1.571 .636 .2 2.088 2.118 4.029 156 947 65.105 .03 150 4430 9870 139 154 371 386 -50 63 56 7 .646 58 2 1.547 .203 -.63 -2.299
14 83 62 70 55 13 7 82 57 71 62 12 2 0 0 16 32 12 31 48 22 20 5 20 14 1.857 .538 .167 1.685 1.671 3.612 156 1073 -73.945 -.03 150 4630 9870 139 154 391 406 -50 63 56 7 .547 58 2 1.828 .169 -.871 -2.563
15 95 68 74 60 21 8 97 60 77 63 23 0 0 0 15 33 16 28 65 25 15 9 29 23 2.625 .381 null 1.166 1.5 4.683 32 171 8.231 .13 60 4860 9860 143 149 419 425 0 69 61 8 .387 61 0 2.584 null -1.37 null
16 82 59 70 57 12 2 82 52 70 62 12 -5 0 0 17 30 11 30 50 12 26 4 14 7 6 .167 null 1.306 1.354 4.089 156 964 -1 -1 150 5030 9870 139 154 431 446 -50 60 58 2 .169 53 -5 5.907 null -2.563 null
17 87 95 71 56 16 39 84 83 74 63 13 27 0 0 26 46 17 31 25 41 8 41 55 40 .41 2.438 2.077 2.635 3.889 3.014 12 104 12.444 .09 50 5210 9880 145 150 454 459 0 96 57 40 2.476 84 27 .404 2.109 1.308 1.077
18 77 67 70 58 7 9 70 54 71 61 0 -4 0 0 20 43 14 27 28 25 9 9 16 -4 .778 1.286 null 3.321 4.2 5.363 32 176 -28.475 -.05 60 5410 9840 141 147 474 480 0 68 59 9 1.306 55 -4 .766 null .385 null
19 88 56 70 54 18 2 87 49 71 59 17 -5 0 0 19 30 13 29 57 16 36 5 20 12 9 .111 null 1.09 1.069 3.514 156 766 -53.569 -.03 150 2030 10090 161 176 131 146 -50 57 55 2 .113 50 -5 8.861 null -3.147 null
20 87 60 68 52 19 8 83 57 69 59 15 5 0 0 19 27 12 29 54 21 36 6 27 20 2.375 .421 .333 1.45 1.333 4.155 156 648 -1 -1 150 2230 10090 161 176 151 166 -50 61 53 8 .428 58 5 2.338 .339 -1.225 -1.563

Total number of rows: 4992

Table truncated, full table size 958 Kbytes.




Supplementary data files not provided
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