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Sample GSM930326 Query DataSets for GSM930326
Status Public on May 12, 2012
Title LCM mock2-4 mucus producing
Sample type RNA
 
Channel 1
Source name pooled aged matched control samples 2x amplified
Organism Mus musculus
Characteristics reference: pooled aged matched control samples 2x amplified
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name mock2-4 mucus producing
Organism Mus musculus
Characteristics time: 2 d
infection: control
cell type: pit
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol model: GenePix 4000A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41289.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 May 11, 2012
Last update date May 12, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL6330
Series (1)
GSE37938 Arrays of time course experiment (2-28 d) laser microdissected samples of H. pylori -infected mice

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 80 201 38 76 42 125 79 191 39 76 41 115 0 0 13 56 5 17 100 100 100 96 167 156 .336 2.976 2.805 2.821 2.888 1.464 32 158 3.744 .87 60 1160 8880 61 67 69 75 0 120 45 74 1.771 114 68 .565 1.669 .825 .739
2 93 214 38 65 55 149 93 217 40 72 55 152 0 0 13 40 10 21 100 100 100 100 204 207 .369 2.709 2.764 2.663 2.583 1.142 12 104 3.06 .92 50 1300 8870 60 65 83 88 0 127 39 89 1.612 129 90 .62 1.645 .689 .718
3 88 158 34 56 54 102 82 155 36 59 48 99 0 0 21 52 7 17 98 96 98 92 156 147 .529 1.889 2.063 1.7 1.719 1.552 52 374 2.086 .91 90 1450 8880 59 68 96 105 0 94 33 61 1.124 92 59 .89 1.227 .169 .296
4 57 131 36 59 21 72 56 104 37 63 20 45 0 0 10 65 6 19 93 93 78 65 93 65 .292 3.429 2.25 2.909 2.727 1.929 32 179 6.043 .71 70 1630 8860 58 65 115 122 0 78 35 43 2.04 62 27 .49 1.339 1.029 .421
5 91 245 34 58 57 187 89 207 35 61 55 149 0 0 23 170 5 16 100 98 100 97 244 204 .305 3.281 2.709 2.854 2.781 1.617 80 377 5.92 .73 100 1740 8870 58 68 125 135 0 146 35 111 1.952 123 89 .512 1.612 .965 .689
6 1184 665 31 52 1153 613 1230 653 33 55 1199 601 0 0 350 272 7 19 100 100 100 100 1766 1800 1.881 .532 .501 .504 .503 1.329 80 408 .55 .95 100 1890 8870 58 68 140 150 0 396 31 365 .316 389 358 3.161 .298 -1.66 -1.745
7 59 79 40 64 19 15 66 76 41 67 26 12 0 0 16 30 13 24 68 28 46 12 34 38 1.267 .789 .462 1.001 .857 2.789 32 158 1.628 .79 60 2030 8860 59 65 156 162 0 47 38 9 .47 45 7 2.129 .275 -1.09 -1.864
8 58 138 46 81 12 57 55 122 47 83 9 41 0 0 11 54 7 19 59 65 28 53 69 50 .211 4.75 4.556 4.773 4.467 2.381 32 170 4.82 .66 60 2180 8860 59 65 171 177 0 82 48 34 2.827 73 24 .354 2.711 1.499 1.439
9 114 178 47 81 67 97 116 162 49 83 69 81 0 0 24 74 9 18 100 87 100 84 164 150 .691 1.448 1.174 1.175 1.33 2.135 32 214 1.905 .8 70 2330 8860 58 65 185 192 0 106 48 58 .862 96 48 1.161 .699 -.215 -.517
10 40 66 43 71 -3 -5 40 68 44 73 -3 -3 0 0 6 14 7 15 3 3 0 0 -8 -6 null null null 1.843 2.036 2.341 32 165 4.953 .37 60 2470 8860 59 65 200 206 0 39 42 -3 null 40 -2 null null null null
11 89 165 42 71 47 94 88 154 43 74 46 83 0 0 8 46 10 17 100 100 100 100 141 129 .5 2 1.804 1.821 1.675 1.492 12 98 2.205 .82 50 2620 8860 59 64 215 220 0 98 42 56 1.19 92 49 .84 1.074 .251 .103
12 46 141 38 67 8 74 46 124 39 68 8 57 0 0 6 60 8 15 50 91 8 75 82 65 .108 9.25 7.125 7.488 8.8 2.192 12 104 8.699 .66 50 2730 8880 61 66 226 231 0 84 40 44 5.505 74 34 .182 4.24 2.461 2.084
13 50 97 36 61 14 36 52 97 37 61 16 36 0 0 4 13 5 15 100 100 75 66 50 52 .389 2.571 2.25 2.473 2.635 1.669 12 68 3.542 .67 40 2890 8870 61 65 243 247 0 58 36 21 1.53 58 21 .653 1.339 .614 .421
14 151 166 35 56 116 110 152 157 35 57 117 101 0 0 32 60 4 11 100 100 100 94 226 218 1.055 .948 .863 .843 .883 1.679 52 301 1.015 .85 80 3050 8860 58 66 257 265 0 99 33 65 .564 93 60 1.772 .514 -.825 -.961
15 119 116 34 52 85 64 124 115 34 54 90 63 0 0 29 35 4 11 100 92 100 84 149 153 1.328 .753 .7 .626 .739 2.126 52 368 .752 .83 90 3200 8870 58 67 271 280 0 69 31 38 .448 68 37 2.232 .417 -1.158 -1.263
16 69 98 32 49 37 49 69 77 33 52 37 28 0 0 12 72 4 13 100 91 100 50 86 65 .755 1.324 .757 .912 .908 2.116 12 104 4.117 .64 50 3360 8860 59 64 289 294 0 58 29 29 .788 46 17 1.269 .45 -.344 -1.151
17 33 49 32 47 1 2 32 48 33 48 0 1 0 0 5 10 4 9 21 21 9 0 3 1 .5 2 null 1.594 2.143 3.493 32 154 4.851 .27 60 3500 8860 59 65 303 309 0 29 28 1 1.19 29 1 .84 null .251 null
18 187 268 33 48 154 220 195 223 33 50 162 175 0 0 65 134 7 12 100 100 100 100 374 337 .7 1.429 1.08 1.388 1.373 1.543 12 94 1.495 .9 50 3600 8860 59 64 313 318 0 159 29 131 .85 133 104 1.176 .643 -.234 -.637
19 30 42 30 43 0 -1 28 41 30 43 -2 -2 0 0 7 10 3 7 18 18 15 12 -1 -4 null null null 1.725 2 3.297 32 170 2.157 .28 60 3790 8860 59 65 332 338 0 25 26 -1 null 24 -1 null null null null
20 35 50 29 46 6 4 33 51 30 46 4 5 0 0 8 9 3 8 53 28 34 3 10 9 1.5 .667 1.25 1.2 1.143 3.503 32 170 3.69 .28 60 3930 8860 59 65 346 352 0 30 27 2 .397 30 3 2.521 .744 -1.334 -.427

Total number of rows: 42624

Table truncated, full table size 8301 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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