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Sample GSM65532 Query DataSets for GSM65532
Status Public on Jul 26, 2005
Title ATCC19609 R5NG 2/9/03 36 h (2)
Sample type RNA
 
Channel 1
Source name 12 h
Organism Streptomyces coelicolor
Characteristics 12 h
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 36 h
Organism Streptomyces coelicolor
Characteristics 36 h
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Strain comparison, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43932.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 Jul 25, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL2620
Series (2)
GSE2995 S. fradiae WT and KOS155-3C R5/No Glucose 02/09/03
GSE4395 Reverse engineering of industrial pharmaceutical-producing actinomycete strains

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
1 709 1115 330 352 379 763 548 901 457 434 218 549 0 0 418 745 873 311 25 66 0 41 1142 767 .497 2.013 2.518 2.545 1.862 6.046 12 98 .042 .07 50 2640 15130 22 27 49 54 -100 1112 351 761 2.008 899 548 .498 2.512 1.006 1.329
2 615 696 315 300 300 396 478 460 326 338 163 160 0 0 313 533 76 171 75 50 53 31 696 323 .758 1.32 .982 1.152 1.053 4.432 32 172 2.982 .39 60 2820 15120 21 27 67 73 -100 694 299 395 1.317 459 160 .759 .979 .397 -.03
3 652 731 348 325 304 406 445 644 351 342 97 319 0 0 477 461 75 133 53 68 43 56 710 416 .749 1.336 3.289 1.218 1.775 3.855 32 170 1.963 .31 60 2960 15120 21 27 81 87 -100 729 324 405 1.332 642 318 .751 3.281 .414 1.714
4 887 738 325 300 562 438 938 740 329 310 613 440 0 0 425 298 77 109 80 86 75 68 1000 1053 1.283 .779 .718 .868 .756 3.586 80 505 .656 .57 110 3120 15110 17 28 94 105 0 736 299 437 .777 738 439 1.286 .716 -.363 -.482
5 849 691 335 309 514 382 830 686 340 315 495 377 0 0 284 254 82 111 96 81 93 75 896 872 1.346 .743 .762 .659 .729 2.935 32 220 .641 .46 70 3270 15120 20 27 111 118 0 689 308 381 .741 684 376 1.349 .76 -.432 -.396
6 743 601 343 323 400 278 756 589 348 327 413 266 0 0 387 229 75 125 71 68 62 53 678 679 1.439 .695 .644 .519 .47 3.2 32 226 2.394 .1 70 3450 15120 20 27 129 136 0 600 322 277 .693 588 265 1.442 .643 -.528 -.638
7 1194 1179 327 322 867 857 1270 1159 330 337 943 837 0 0 511 402 76 120 87 97 87 93 1724 1780 1.012 .988 .888 1.016 .897 2.505 80 396 .852 .67 100 3610 15120 19 29 144 154 0 1176 321 855 .986 1156 835 1.014 .885 -.02 -.176
8 1058 1167 329 321 729 846 1036 1129 332 328 707 808 0 0 327 377 78 110 100 100 92 100 1575 1515 .862 1.16 1.143 1.213 1.259 2.049 52 328 1.183 .7 90 3750 15130 20 29 158 167 0 1164 320 844 1.158 1126 806 .864 1.14 .211 .189
9 972 1053 344 337 628 716 972 955 346 340 628 618 0 0 381 392 77 120 90 93 87 90 1344 1246 .877 1.14 .984 1.034 .991 2.708 32 232 1.064 .53 70 3920 15140 22 29 176 183 0 1050 336 714 1.137 953 616 .879 .982 .186 -.027
10 967 791 341 304 626 487 1039 833 383 353 698 529 0 0 265 275 220 204 91 83 66 66 1113 1227 1.285 .778 .758 .767 .688 1.988 12 104 .917 .65 50 4080 15140 23 28 193 198 0 789 303 486 .776 831 528 1.289 .756 -.366 -.403
11 1223 1086 295 280 928 806 1283 1141 317 304 988 861 0 0 627 502 137 146 86 88 80 80 1734 1849 1.151 .869 .871 .958 .884 2.816 52 368 .736 .7 90 4250 15130 20 29 208 217 0 1083 279 804 .866 1138 859 1.154 .869 -.207 -.202
12 1151 1017 318 289 833 728 1222 1101 327 301 904 812 0 0 576 460 100 121 88 86 82 76 1561 1716 1.144 .874 .898 .957 .867 3.383 52 294 .698 .71 80 4390 15130 21 29 223 231 0 1015 288 726 .872 1098 810 1.147 .896 -.198 -.158
13 1032 1167 312 285 720 882 922 1102 314 295 610 817 0 0 540 544 73 102 88 93 82 92 1602 1427 .816 1.225 1.339 1.292 1.058 2.849 80 460 1.178 .71 100 4570 15140 21 31 240 250 0 1164 284 880 1.222 1099 815 .818 1.336 .289 .418
14 1084 985 328 319 756 666 1153 988 333 331 825 669 0 0 449 464 81 121 91 88 87 77 1422 1494 1.135 .881 .811 .917 .835 3.361 80 431 .932 .69 100 4740 15160 23 33 257 267 0 983 318 664 .879 986 667 1.138 .809 -.186 -.306
15 1073 875 320 313 753 562 1151 878 326 327 831 565 0 0 311 295 87 121 96 93 90 87 1315 1396 1.34 .746 .68 .774 .757 2.315 32 224 .769 .66 70 4890 15160 24 31 273 280 0 873 312 561 .745 876 564 1.343 .678 -.426 -.56
16 892 903 297 284 595 619 965 917 301 290 668 633 0 0 381 355 83 104 88 92 86 82 1214 1301 .961 1.04 .948 .858 .947 2.465 52 348 .957 .65 90 5050 15150 22 31 288 297 0 901 283 617 1.038 915 631 .964 .945 .054 -.081
17 1164 1235 324 305 840 930 1107 1226 330 315 783 921 0 0 558 632 84 123 93 95 87 86 1770 1704 .903 1.107 1.176 1.093 1.085 2.908 80 444 1.18 .75 100 5200 15160 23 33 303 313 0 1232 304 928 1.104 1223 919 .905 1.173 .143 .231
18 1212 1355 317 312 895 1043 1286 1310 324 323 969 998 0 0 620 646 88 117 86 100 80 92 1938 1967 .858 1.165 1.03 1.207 1.043 3.404 52 294 1.274 .67 80 5370 15170 25 33 321 329 0 1352 311 1040 1.163 1307 996 .86 1.027 .217 .039
19 882 1102 318 320 564 782 984 1170 321 325 666 850 0 0 363 391 75 124 84 92 82 86 1346 1516 .721 1.387 1.276 1.418 1.244 2.148 52 369 1.419 .72 90 5520 15160 23 32 335 344 0 1099 319 780 1.383 1167 848 .723 1.273 .468 .348
20 988 1001 333 314 655 687 1000 1058 336 332 667 744 0 0 302 304 77 122 93 96 93 87 1342 1411 .953 1.049 1.115 1.143 1.112 2.825 32 236 .95 .56 70 5680 15170 25 32 352 359 0 999 313 685 1.046 1055 742 .956 1.113 .065 .154

Total number of rows: 11520

Table truncated, full table size 2599 Kbytes.




Supplementary data files not provided
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