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Sample GSM930333 Query DataSets for GSM930333
Status Public on May 12, 2012
Title LCM SS2-5 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 SS2-5 mucus producing
Organism Mus musculus
Characteristics time: 2 d
infection: infected
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/2003-06/42030.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
1 222 561 149 317 73 244 220 577 152 326 71 260 0 0 23 60 38 77 91 100 41 91 317 331 .299 3.342 3.662 3.412 3.247 1.604 12 98 6.965 .37 50 1020 8920 58 63 67 72 0 790 447 344 4.71 813 366 .212 5.16 2.236 2.367
2 336 479 135 275 201 204 324 487 141 283 189 212 0 0 38 38 29 57 100 100 100 100 405 401 .985 1.015 1.122 1.013 1.066 1.301 12 100 1.066 .76 50 1140 8920 58 63 79 84 0 675 387 287 1.43 686 299 .699 1.58 .516 .66
3 398 626 116 238 282 388 375 572 123 242 259 334 0 0 127 161 39 53 100 100 96 100 670 593 .727 1.376 1.29 1.402 1.343 1.498 32 226 1.226 .81 70 1290 8920 57 64 93 100 0 882 335 547 1.939 806 471 .516 1.817 .955 .862
4 204 412 106 206 98 206 209 409 108 207 103 203 0 0 34 73 22 37 96 100 90 96 304 306 .476 2.102 1.971 2.118 2.148 1.641 32 192 2.449 .79 70 1420 8930 58 65 106 113 0 581 290 290 2.962 576 286 .338 2.777 1.566 1.474
5 264 510 106 209 158 301 257 488 112 220 151 279 0 0 44 98 33 67 100 100 100 100 459 430 .525 1.905 1.848 1.875 1.939 1.291 32 218 2.134 .83 70 1570 8890 54 61 121 128 0 719 294 424 2.684 688 393 .373 2.603 1.425 1.38
6 9205 829 98 183 9107 646 9028 819 102 191 8930 636 0 0 3796 282 28 54 100 97 98 97 9753 9566 14.098 .071 .071 .073 .073 1.606 80 482 .065 .92 100 1720 8900 54 64 135 145 0 1168 258 910 .1 1154 896 10.005 .1 -3.323 -3.317
7 356 355 93 167 263 188 377 375 95 169 284 208 0 0 74 72 20 30 100 96 96 93 451 492 1.399 .715 .732 .672 .78 1.539 32 172 .762 .89 60 1890 8910 57 63 154 160 0 500 235 265 1.007 528 293 .993 1.032 .01 .045
8 218 315 90 167 128 148 212 299 95 168 122 132 0 0 26 45 24 33 100 100 100 100 276 254 .865 1.156 1.082 1.13 1.059 1.365 12 104 1.456 .75 50 2040 8900 56 61 169 174 0 444 235 209 1.629 421 186 .614 1.525 .704 .608
9 630 464 87 149 543 315 654 519 89 153 567 370 0 0 213 158 18 31 100 96 100 93 858 937 1.724 .58 .653 .558 .586 1.673 32 172 .592 .93 60 2190 8900 56 62 184 190 0 654 210 444 .817 731 521 1.223 .919 -.291 -.121
10 108 148 87 147 21 1 95 151 88 150 8 4 0 0 46 26 18 26 37 15 21 6 22 12 21 .048 .5 .628 .717 8.007 32 166 .19 .13 60 2320 8890 55 61 197 203 0 209 207 1 .067 213 6 14.904 .705 -3.898 -.505
11 600 281 91 157 509 124 633 292 91 157 542 135 0 0 139 79 16 28 100 91 100 75 633 677 4.105 .244 .249 .227 .265 1.549 12 98 .295 .79 50 2470 8890 55 60 212 217 0 396 221 175 .343 411 190 2.913 .351 -1.543 -1.511
12 154 237 89 145 65 92 152 230 91 148 63 85 0 0 23 33 19 29 100 100 83 91 157 148 .707 1.415 1.349 1.433 1.166 1.699 12 68 1.742 .69 40 2620 8900 57 61 228 232 0 334 204 130 1.994 324 120 .501 1.901 .996 .927
13 142 219 85 153 57 66 139 220 88 151 54 67 0 0 19 35 20 27 91 91 91 66 123 121 .864 1.158 1.241 1.259 1.253 1.601 12 68 1.852 .66 40 2770 8900 57 61 243 247 0 309 216 93 1.632 310 94 .613 1.748 .706 .806
14 1349 718 95 152 1254 566 1348 750 111 158 1253 598 0 0 445 232 102 37 100 100 100 100 1820 1851 2.216 .451 .477 .43 .452 1.356 32 198 .456 .9 70 2910 8900 55 62 255 262 0 1012 214 798 .636 1057 843 1.572 .672 -.653 -.572
15 1371 526 91 146 1280 380 1097 464 97 149 1006 318 0 0 1037 262 48 29 100 100 100 98 1660 1324 3.368 .297 .316 .313 .322 1.623 52 293 .236 .85 80 3040 8910 56 64 268 276 0 741 206 535 .418 654 448 2.391 .445 -1.257 -1.167
16 284 288 89 149 195 139 298 288 93 149 209 139 0 0 75 68 25 30 96 93 93 84 334 348 1.403 .713 .665 .689 .721 2.35 32 176 .771 .79 60 3200 8920 58 64 285 291 0 406 210 196 1.004 406 196 .996 .937 .006 -.094
17 94 153 90 149 4 4 91 152 94 153 1 3 0 0 23 31 23 32 9 12 6 3 8 4 1 1 3 1.171 1 4.566 32 170 1.034 .78 60 3340 8890 55 61 299 305 0 216 210 6 1.409 214 4 .71 4.227 .495 2.08
18 1185 932 94 149 1091 783 1288 908 96 150 1194 759 0 0 594 475 21 29 100 100 100 91 1874 1953 1.393 .718 .636 .602 .732 2.474 12 98 .741 .9 50 3500 8880 54 59 315 320 0 1313 210 1103 1.011 1279 1069 .989 .896 .016 -.159
19 128 147 92 149 36 -2 109 142 135 204 17 -7 0 0 57 32 302 437 0 0 0 0 34 10 null null null .907 1.286 5.228 32 170 1.813 .88 60 3640 8890 55 61 329 335 0 207 210 -3 null 200 -10 null null null null
20 131 161 88 146 43 15 115 154 89 147 27 8 0 0 64 45 18 26 59 28 31 21 58 35 2.867 .349 .296 1.092 .809 3.024 32 170 .691 .58 60 3780 8890 55 61 343 349 0 227 206 21 .492 217 11 2.035 .417 -1.025 -1.26

Total number of rows: 42624

Table truncated, full table size 9000 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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