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Sample GSM150602 Query DataSets for GSM150602
Status Public on Dec 15, 2006
Title NSH79 17-3 1wk: S, 2C
Sample type genomic
 
Channel 1
Source name NSH79 17 input 2 S, 2C
Organism Helicobacter pylori
Characteristics NSH79 17 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 NSH79 17-3 1wk; S, 2C
Organism Helicobacter pylori
Characteristics output mouse NSH79 17-3 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 = 920, 8160; 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 = 31.09; Parameter Scan Time = 10:52:00; Parameter PMT Volts = 330; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 44043; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.43; 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 = 31.09; Parameter Scan Time = 10:52:00; Parameter PMT Volts = 460; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 44051; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.79; 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/2004-04/50956.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)
GSE6529 NSH79 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 85 83 31 35 54 48 89 79 31 36 58 44 0 0 29 31 3 8 100 88 98 80 102 102 1.125 .889 .759 .862 .891 2.654 80 619 .943 .72 110 2180 9260 104 115 120 131 0 50 21 29 .533 47 26 1.876 .455 -.908 -1.136
2 79 82 31 35 48 47 82 77 31 36 51 42 0 0 32 34 3 7 90 85 86 79 95 93 1.021 .979 .824 .978 .933 2.625 120 716 .985 .71 130 2390 9280 105 118 140 153 0 49 21 28 .587 46 25 1.703 .494 -.768 -1.018
3 68 74 31 35 37 39 63 70 32 35 32 35 0 0 28 29 3 7 98 85 89 80 76 67 .949 1.054 1.094 1.164 1.213 2.746 120 660 1.165 .69 130 2590 9270 104 117 160 173 0 44 21 23 .632 42 21 1.582 .656 -.662 -.609
4 91 102 32 35 59 67 90 94 32 36 58 59 0 0 45 55 3 8 90 88 85 78 126 117 .881 1.136 1.017 1.216 1.195 2.83 120 629 1.259 .81 130 2790 9280 105 118 180 193 0 61 21 40 .681 56 35 1.468 .61 -.554 -.713
5 79 115 32 35 47 80 73 105 32 36 41 70 0 0 36 55 3 7 95 97 94 95 127 111 .588 1.702 1.707 1.813 1.741 2.443 156 757 1.834 .78 140 3000 9270 104 118 201 215 0 69 21 48 1.021 63 42 .98 1.024 .03 .034
6 32 35 32 35 0 0 32 35 32 36 0 0 0 0 3 7 3 7 16 12 1 1 0 0 null null null 1.747 1.708 3.31 156 850 33.692 .05 150 3200 9260 102 117 220 235 -50 21 21 0 null 21 0 null null null null
7 85 108 32 35 53 73 82 100 33 38 50 65 0 0 39 58 15 28 74 69 63 51 126 115 .726 1.377 1.3 1.429 1.466 2.902 120 625 1.558 .75 130 3400 9270 104 117 241 254 0 65 21 44 .826 60 39 1.211 .78 -.276 -.359
8 41 62 32 34 9 28 41 61 33 36 9 27 0 0 7 14 14 25 17 55 0 6 37 36 .321 3.111 3 2.87 3.222 2.884 156 766 3.802 .59 140 3590 9270 104 118 260 274 0 37 20 17 1.866 37 16 .536 1.799 .9 .847
9 80 97 32 33 48 64 72 94 32 34 40 61 0 0 34 55 3 7 96 83 95 78 112 101 .75 1.333 1.525 1.175 1.241 3.463 80 497 1.755 .65 100 3790 9260 105 115 282 292 0 58 20 38 .8 56 37 1.251 .914 -.323 -.129
10 76 109 33 34 43 75 79 107 33 35 46 73 0 0 24 40 5 7 92 100 86 98 118 119 .573 1.744 1.587 1.984 1.56 3.166 52 420 2.029 .7 90 3990 9240 103 112 302 311 0 65 20 45 1.046 64 44 .956 .952 .065 -.072
11 40 43 33 33 7 10 39 41 33 34 6 8 0 0 6 10 5 7 55 52 26 28 17 14 .7 1.429 1.333 1.665 1.607 2.996 80 520 2.621 .4 100 4190 9250 104 114 322 332 0 26 20 6 .857 25 5 1.167 .8 -.223 -.323
12 44 49 32 33 12 16 43 48 32 34 11 15 0 0 9 16 3 6 76 71 65 53 28 26 .75 1.333 1.364 1.401 1.4 2.824 80 573 2.429 .54 110 4410 9250 103 114 343 354 0 29 20 10 .8 29 9 1.251 .818 -.323 -.29
13 40 43 32 33 8 10 40 42 32 34 8 9 0 0 5 9 4 6 75 60 47 39 18 17 .8 1.25 1.125 1.208 1.2 2.691 120 748 2.568 .43 130 4590 9260 103 116 360 373 0 26 20 6 .75 25 5 1.334 .675 -.416 -.568
14 36 35 32 33 4 2 37 34 32 33 5 1 0 0 4 7 4 6 51 23 17 7 6 6 2 .5 .2 1.05 1 2.943 156 941 4.69 .22 150 4800 9250 101 116 380 395 -50 21 20 1 .3 20 1 3.335 .12 -1.738 -3.06
15 39 37 32 33 7 4 39 36 32 33 7 3 0 0 5 8 3 6 73 32 50 14 11 10 1.75 .571 .429 1.05 1.125 2.816 156 832 2.596 .3 150 5000 9250 101 116 400 415 -50 22 20 2 .343 22 2 2.918 .257 -1.545 -1.96
16 38 39 32 33 6 6 37 37 32 34 5 4 0 0 6 15 3 12 60 17 37 3 12 9 1 1 .8 1.33 1.108 3.497 156 798 72.977 .04 150 5200 9250 101 116 420 435 -50 23 20 4 .6 22 2 1.668 .48 -.738 -1.06
17 40 53 32 33 8 20 39 45 33 35 7 12 0 0 10 26 4 15 59 44 42 27 28 19 .4 2.5 1.714 1.943 1.794 3.794 120 621 6.198 .39 120 5390 9260 104 116 441 453 0 32 20 12 1.499 27 7 .667 1.028 .584 .04
18 47 73 33 34 14 39 44 62 33 35 11 28 0 0 12 37 5 12 75 78 51 53 53 39 .359 2.786 2.545 2.371 2.668 2.991 52 414 5.388 .51 90 5630 9260 105 114 466 475 0 44 20 23 1.67 37 17 .599 1.526 .74 .61
19 39 45 31 35 8 10 39 44 31 36 8 9 0 0 4 11 3 8 84 50 61 22 18 17 .8 1.25 1.125 1.449 1.472 2.783 120 708 4.868 .3 130 2200 9480 125 138 121 134 0 27 21 6 .75 26 5 1.334 .675 -.416 -.568
20 40 49 31 35 9 14 40 47 32 36 9 12 0 0 5 12 3 7 89 64 67 40 23 21 .643 1.556 1.333 1.223 1.5 3.253 120 562 3.688 .43 130 2400 9470 124 137 141 154 0 29 21 8 .933 28 7 1.072 .8 -.1 -.323

Total number of rows: 4992

Table truncated, full table size 936 Kbytes.




Supplementary data files not provided
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