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Sample GSM930319 Query DataSets for GSM930319
Status Public on May 12, 2012
Title LCM SS2-5 chief
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 chief
Organism Mus musculus
Characteristics time: 2 d
infection: infected
cell type: chief
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/2003-06/42031.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
1 578 1720 359 984 219 736 582 1752 367 993 223 768 0 0 90 189 78 150 93 100 68 93 955 991 .298 3.361 3.444 3.532 3.484 1.64 32 211 3.634 .76 70 960 9000 65 72 60 67 0 4123 2359 1764 8.056 4199 1841 .124 8.255 3.01 3.045
2 748 1698 336 914 412 784 739 1683 339 936 403 769 0 0 91 183 71 133 100 100 100 100 1196 1172 .526 1.903 1.908 1.887 2.032 1.38 12 104 2.101 .82 50 1100 8980 64 69 75 80 0 4070 2191 1879 4.561 4034 1843 .219 4.574 2.189 2.193
3 701 1642 302 854 399 788 639 1550 310 862 337 696 0 0 246 375 64 119 98 98 92 98 1187 1033 .506 1.975 2.065 2.114 2.254 1.456 52 342 1.993 .88 90 1250 8990 63 72 88 97 0 3936 2047 1889 4.734 3715 1668 .211 4.95 2.243 2.308
4 434 1332 277 766 157 566 438 1315 279 773 161 549 0 0 98 191 61 112 90 96 62 96 723 710 .277 3.605 3.41 3.299 4.03 1.933 32 194 3.95 .63 70 1370 9010 66 73 101 108 0 3193 1836 1357 8.641 3152 1316 .116 8.173 3.111 3.031
5 522 1484 258 723 264 761 512 1484 267 732 254 761 0 0 134 320 61 131 95 100 85 96 1025 1015 .347 2.883 2.996 3.153 2.869 1.937 80 397 3.117 .84 100 1540 8990 63 73 117 127 0 3557 1733 1824 6.909 3557 1824 .145 7.181 2.789 2.844
6 6224 1910 240 657 5984 1253 6573 1916 255 670 6333 1259 0 0 3141 501 145 126 98 100 95 97 7237 7592 4.776 .209 .199 .254 .209 1.964 80 394 .182 .92 100 1680 8980 62 72 131 141 0 4578 1575 3003 .502 4593 3018 1.992 .477 -.995 -1.069
7 547 1096 224 600 323 496 603 1142 233 620 379 542 0 0 161 243 54 112 90 88 88 84 819 921 .651 1.536 1.43 1.439 1.492 2.076 52 274 1.641 .87 80 1850 9000 65 73 149 157 0 2627 1438 1189 3.681 2737 1299 .272 3.428 1.88 1.777
8 357 1020 227 575 130 445 375 1020 238 608 148 445 0 0 81 166 64 138 83 100 58 83 575 593 .292 3.423 3.007 3.402 3.147 1.771 12 104 3.34 .74 50 1980 8980 64 69 163 168 0 2445 1378 1067 8.205 2445 1067 .122 7.207 3.036 2.849
9 850 1287 221 530 629 757 879 1314 221 536 658 784 0 0 260 302 51 81 100 100 100 100 1386 1442 .831 1.203 1.191 1.23 1.223 1.395 32 158 1.199 .93 60 2150 8990 65 71 180 186 0 3085 1270 1814 2.885 3150 1879 .347 2.856 1.528 1.514
10 222 480 208 499 14 -19 220 464 210 497 12 -35 0 0 41 77 51 67 18 18 0 0 -5 -23 null null null .8 .899 3.636 32 161 10.143 .11 60 2270 8970 63 69 192 198 0 1151 1196 -46 null 1112 -84 null null null null
11 652 780 204 456 448 324 656 805 207 462 452 349 0 0 77 98 43 73 100 100 100 100 772 801 1.383 .723 .772 .698 .766 1.328 12 98 .851 .87 50 2440 8970 63 68 209 214 0 1870 1093 777 1.734 1930 837 .577 1.851 .794 .888
12 222 700 173 423 49 277 222 678 176 424 49 255 0 0 51 93 37 53 58 100 41 100 326 304 .177 5.653 5.204 6.248 4.84 3.36 12 104 5.117 .46 50 2580 8980 64 69 223 228 0 1678 1014 664 13.55 1625 611 .074 12.474 3.76 3.641
13 271 669 164 395 107 274 268 657 175 396 104 262 0 0 53 87 47 54 91 100 50 100 381 366 .391 2.561 2.519 2.824 2.343 1.807 12 104 2.913 .61 50 2730 8980 64 69 238 243 0 1604 947 657 6.138 1575 628 .163 6.038 2.618 2.594
14 1433 1097 180 405 1253 692 1431 1031 208 431 1251 626 0 0 319 264 154 136 100 100 100 100 1945 1877 1.811 .552 .5 .54 .514 1.41 32 198 .521 .88 70 2870 8970 62 69 251 258 0 2629 971 1659 1.324 2471 1500 .755 1.199 .405 .262
15 1232 974 168 375 1064 599 1053 960 176 387 885 585 0 0 856 297 51 79 100 100 98 98 1663 1470 1.776 .563 .661 .689 .648 1.705 52 339 .443 .87 90 2990 8980 62 71 262 271 0 2335 899 1436 1.349 2301 1402 .741 1.584 .432 .664
16 409 619 164 382 245 237 410 619 170 386 246 237 0 0 90 97 42 68 100 96 93 81 482 483 1.034 .967 .963 .942 .953 1.899 32 176 1.117 .79 60 3140 9000 66 72 279 285 0 1484 916 568 2.319 1484 568 .431 2.309 1.213 1.207
17 163 351 146 358 17 -7 146 350 155 371 0 -8 0 0 50 67 43 88 21 6 12 0 10 -8 null null null 1.615 1.279 7.611 32 170 .838 .41 60 3290 8970 63 69 294 300 0 841 858 -17 null 839 -19 null null null null
18 2125 1106 156 357 1969 749 2284 1079 158 362 2128 722 0 0 1112 481 36 57 100 91 100 83 2718 2850 2.629 .38 .339 .311 .404 1.961 12 104 .414 .95 50 3460 8970 63 68 311 316 0 2651 856 1795 .912 2586 1731 1.097 .813 -.133 -.298
19 173 375 150 351 23 24 164 384 150 352 14 33 0 0 68 101 35 51 31 34 15 15 47 47 .958 1.043 2.357 1.619 1.831 2.664 32 170 2.125 .48 60 3590 8970 63 69 324 330 0 899 841 58 2.501 920 79 .4 5.65 1.323 2.498
20 174 392 155 347 19 45 158 373 161 350 3 26 0 0 64 101 52 100 18 28 12 6 64 29 .422 2.368 8.667 1.49 1.442 5.675 32 170 4.135 .26 60 3730 8970 63 69 338 344 0 940 832 108 5.677 894 62 .176 20.774 2.505 4.377

Total number of rows: 42624

Table truncated, full table size 8975 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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