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Sample GSM930347 Query DataSets for GSM930347
Status Public on May 12, 2012
Title LCM mock7-2 parietal
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 mock7-2 parietal
Organism Mus musculus
Characteristics time: 7 d
infection: control
cell type: parietal
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/2003-05/40618.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 65 113 45 69 20 44 68 112 45 70 23 43 0 0 12 27 5 6 84 88 80 88 64 66 .455 2.2 1.87 2.036 1.87 1.428 52 282 2.26 .86 80 1270 8640 68 76 87 95 0 89 55 35 1.742 89 34 .574 1.48 .8 .566
2 74 116 44 66 30 50 74 116 45 68 30 50 0 0 5 9 7 10 100 100 100 100 80 80 .6 1.667 1.667 1.652 1.557 1.278 12 93 1.666 .91 50 1390 8630 68 73 100 105 0 92 52 40 1.319 92 40 .758 1.319 .4 .4
3 75 114 41 63 34 51 75 108 41 64 34 45 0 0 18 29 5 6 96 98 90 95 85 79 .667 1.5 1.324 1.509 1.5 1.48 80 425 1.519 .93 100 1530 8640 67 77 112 122 0 90 50 40 1.187 85 36 .842 1.048 .248 .067
4 60 88 40 63 20 25 60 90 41 63 20 27 0 0 6 12 4 6 100 93 96 81 45 47 .8 1.25 1.35 1.218 1.35 1.633 32 194 1.756 .83 70 1670 8650 69 76 127 134 0 70 50 20 .99 71 21 1.011 1.069 -.015 .096
5 82 126 39 61 43 65 81 121 40 61 42 60 0 0 24 35 4 7 98 100 96 96 108 102 .662 1.512 1.429 1.569 1.536 1.614 80 405 1.57 .93 100 1820 8640 67 77 141 151 0 100 48 51 1.197 96 47 .836 1.131 .259 .178
6 298 144 39 60 259 84 299 144 40 60 260 84 0 0 47 23 5 5 100 100 100 100 343 344 3.083 .324 .323 .315 .32 1.244 52 327 .32 .94 90 1960 8630 66 75 155 164 0 114 47 66 .257 114 66 3.895 .256 -1.962 -1.967
7 70 96 38 56 32 40 70 93 38 57 32 37 0 0 7 12 4 7 100 100 100 100 72 69 .8 1.25 1.156 1.215 1.2 1.311 32 172 1.332 .9 60 2120 8650 70 76 173 179 0 76 44 32 .99 74 29 1.011 .915 -.015 -.128
8 54 84 35 48 19 36 49 82 37 51 14 34 0 0 11 14 7 10 100 100 41 100 55 48 .528 1.895 2.429 2.071 2.036 1.413 12 68 1.624 .82 40 2290 8640 70 74 191 195 0 66 38 28 1.5 65 27 .667 1.923 .585 .943
9 88 95 33 46 55 49 89 95 33 46 56 49 0 0 13 15 3 5 100 100 100 100 104 105 1.122 .891 .875 .864 .88 1.233 32 199 .916 .94 70 2430 8640 68 75 203 210 0 75 36 39 .705 75 39 1.418 .693 -.504 -.53
10 32 46 33 47 -1 -1 32 45 33 47 -1 -2 0 0 3 5 3 4 6 9 3 6 -2 -3 null null null 1.189 1 2.469 32 154 3.755 .2 60 2550 8630 68 74 216 222 0 36 37 -1 null 36 -2 null null null null
11 65 69 34 49 31 20 66 65 34 49 32 16 0 0 14 13 4 5 96 87 90 81 51 48 1.55 .645 .5 .593 .641 1.906 32 164 .764 .87 60 2720 8630 68 74 233 239 0 55 39 16 .511 51 13 1.958 .396 -.969 -1.337
12 44 63 34 48 10 15 44 62 34 47 10 14 0 0 4 8 4 5 100 91 75 75 25 24 .667 1.5 1.4 1.348 1.45 1.712 12 98 1.836 .76 50 2870 8630 68 73 248 253 0 50 38 12 1.187 49 11 .842 1.108 .248 .148
13 39 59 33 47 6 12 40 59 33 47 7 12 0 0 4 5 3 5 66 91 50 75 18 19 .5 2 1.714 2.017 1.833 2.994 12 68 2.148 .56 40 3010 8640 70 74 263 267 0 47 37 9 1.583 47 9 .632 1.357 .663 .441
14 85 91 33 47 52 44 90 97 34 48 57 50 0 0 33 25 5 6 88 90 82 86 96 107 1.182 .846 .877 .939 .884 1.556 52 272 .818 .93 80 3150 8630 67 75 275 283 0 72 37 35 .67 77 40 1.493 .694 -.578 -.526
15 92 76 33 48 59 28 92 75 34 48 59 27 0 0 10 8 4 4 100 100 100 100 87 86 2.107 .475 .458 .46 .473 1.333 32 199 .512 .87 70 3270 8640 68 75 287 294 0 60 38 22 .376 59 21 2.662 .362 -1.412 -1.465
16 48 68 33 47 15 21 49 68 33 47 16 21 0 0 5 7 3 4 96 100 96 93 36 37 .714 1.4 1.313 1.379 1.414 1.61 32 218 1.595 .77 70 3430 8640 68 75 303 310 0 54 37 17 1.108 54 17 .902 1.039 .148 .055
17 34 47 33 47 1 0 34 48 33 47 1 1 0 0 4 5 3 4 21 15 6 0 1 2 null null 1 1.254 2 2.581 32 176 2.302 .12 60 3580 8630 68 74 319 325 0 37 37 0 null 38 1 null .792 null -.337
18 117 83 33 45 84 38 119 88 33 45 86 43 0 0 55 20 4 5 100 100 100 83 122 129 2.211 .452 .5 .489 .443 1.484 12 98 .424 .93 50 3740 8620 67 72 335 340 0 66 36 30 .358 70 34 2.792 .396 -1.481 -1.337
19 34 44 32 43 2 1 33 44 32 43 1 1 0 0 4 4 3 4 21 18 15 6 3 2 2 .5 1 1.327 1.125 2.527 32 170 1.265 .34 60 3870 8620 67 73 348 354 0 35 34 1 .396 35 1 2.526 .792 -1.337 -.337
20 32 39 30 37 2 2 32 39 30 37 2 2 0 0 4 4 3 5 37 12 15 3 4 4 1 1 1 .784 1 3.029 32 170 1.479 .51 60 4020 8620 67 73 363 369 0 31 29 2 .792 31 2 1.263 .792 -.337 -.337

Total number of rows: 42624

Table truncated, full table size 8153 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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