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Sample GSM65527 Query DataSets for GSM65527
Status Public on Jul 26, 2005
Title RUS R5NG 2/9/03 24 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 24 h
Organism Streptomyces coelicolor
Characteristics 24 h
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Strain comparison, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43938.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
1 370 435 298 225 72 210 320 283 296 253 22 58 0 0 177 335 73 160 28 31 18 25 282 80 .343 2.917 2.636 1.41 1.531 5.189 32 127 5.306 .24 60 1990 16220 34 40 24 30 -100 445 230 215 2.982 289 59 .335 2.696 1.576 1.431
2 458 656 305 214 153 442 376 607 321 248 71 393 0 0 223 367 99 155 41 66 25 58 595 464 .346 2.889 5.535 3.103 4.992 4.516 12 68 5.419 .18 40 2160 16230 36 40 42 46 -100 671 219 452 2.954 621 402 .339 5.66 1.563 2.501
3 492 669 325 254 167 415 376 580 354 321 51 326 0 0 273 410 126 349 33 50 25 33 582 377 .402 2.485 6.392 1.93 2.351 4.546 12 68 5.514 .25 40 2330 16230 36 40 59 63 -100 684 260 424 2.541 593 333 .394 6.536 1.345 2.708
4 847 632 292 228 555 404 955 640 304 229 663 412 0 0 402 245 99 90 80 90 76 80 959 1075 1.374 .728 .621 .715 .695 2.34 52 364 .621 .64 90 2490 16210 31 40 72 81 0 646 233 413 .744 654 421 1.344 .635 -.426 -.654
5 685 327 288 238 397 89 692 312 324 242 404 74 0 0 199 131 149 103 83 41 83 25 486 478 4.461 .224 .183 .264 .358 3.819 12 104 .233 .42 50 2640 16210 33 38 89 94 0 334 243 91 .229 319 76 4.363 .187 -2.125 -2.417
6 752 477 275 209 477 268 792 483 316 246 517 274 0 0 257 157 179 129 75 83 66 50 745 791 1.78 .562 .53 .455 .53 3.599 12 68 .392 .51 40 2830 16210 34 38 109 113 0 488 214 274 .574 494 280 1.741 .542 -.8 -.884
7 1029 757 256 202 773 555 1126 731 257 208 870 529 0 0 460 273 68 82 88 92 85 91 1328 1399 1.393 .718 .608 .736 .645 2.787 80 411 .604 .73 100 2960 16200 30 40 119 129 0 774 207 567 .734 747 541 1.362 .622 -.446 -.686
8 771 1163 245 202 526 961 785 589 254 216 540 387 0 0 342 4012 85 82 88 86 76 80 1487 927 .547 1.827 .717 .97 .725 3.951 52 291 31.236 .21 80 3120 16200 31 39 136 144 0 1189 207 983 1.868 602 396 .535 .733 .902 -.449
9 620 319 291 202 329 117 587 340 328 224 296 138 0 0 190 137 173 122 83 58 33 25 446 434 2.812 .356 .466 .605 .658 1.968 12 68 .202 .3 40 3260 16210 34 38 152 156 0 326 207 120 .364 348 141 2.75 .477 -1.46 -1.069
10 366 252 286 210 80 42 293 240 288 216 7 30 0 0 232 117 67 79 38 35 27 15 122 37 1.905 .525 4.286 .548 .667 5.18 80 408 .207 .18 100 3480 16200 30 40 171 181 -50 258 215 43 .537 245 31 1.863 4.382 -.898 2.132
11 967 924 291 228 676 696 976 942 299 241 685 714 0 0 594 461 83 118 81 87 75 78 1372 1399 .971 1.03 1.042 1.067 .924 3.098 80 414 .834 .6 100 3610 16200 30 40 184 194 0 945 233 712 1.053 963 730 .95 1.066 .074 .092
12 979 924 286 216 693 708 1099 1028 291 229 813 812 0 0 584 449 100 97 73 86 69 78 1401 1625 .979 1.022 .999 1.103 .947 3.569 52 297 .775 .67 80 3770 16200 31 39 201 209 0 945 221 724 1.045 1051 830 .957 1.021 .063 .03
13 797 671 234 211 563 460 701 611 251 220 467 400 0 0 459 383 129 101 81 81 75 75 1023 867 1.224 .817 .857 .951 .954 2.917 32 176 .667 .59 60 3930 16200 32 38 218 224 0 686 216 470 .835 625 409 1.197 .876 -.259 -.191
14 861 801 259 206 602 595 929 795 263 217 670 589 0 0 442 381 81 89 83 91 75 82 1197 1259 1.012 .988 .879 .991 .892 2.797 80 475 .893 .65 110 4090 16200 29 40 231 242 0 819 211 608 1.011 813 602 .99 .899 .015 -.154
15 702 551 217 191 485 360 756 557 236 210 539 366 0 0 271 229 180 133 76 80 69 61 845 905 1.347 .742 .679 .762 .695 3.299 52 339 .517 .46 90 4250 16210 31 40 248 257 0 563 195 368 .759 570 374 1.318 .694 -.398 -.526
16 772 618 273 234 499 384 797 561 379 273 524 327 0 0 367 216 400 165 66 91 25 50 883 851 1.299 .77 .624 .513 .452 2.175 12 98 .624 .41 50 4440 16200 32 37 269 274 0 632 239 393 .787 574 334 1.271 .638 -.346 -.648
17 1023 877 277 210 746 667 1131 921 279 216 854 711 0 0 469 407 64 78 84 88 82 82 1413 1565 1.118 .894 .833 .852 .911 1.915 52 330 .799 .74 90 4560 16200 30 39 279 288 0 897 215 682 .914 942 727 1.094 .851 -.129 -.232
18 1116 1239 285 217 831 1022 1153 1202 287 222 868 985 0 0 449 635 68 80 94 98 90 92 1853 1853 .813 1.23 1.135 1.104 1.194 2.183 52 253 1.363 .76 80 4730 16210 32 40 297 305 0 1267 222 1045 1.257 1229 1007 .795 1.16 .331 .215
19 501 514 274 227 227 287 420 522 279 235 146 295 0 0 270 260 70 88 62 71 52 62 514 441 .791 1.264 2.021 1.219 1.167 3.324 80 411 1.081 .65 100 4870 16190 29 39 310 320 0 526 232 293 1.293 534 302 .774 2.066 .37 1.047
20 574 479 272 230 302 249 608 429 282 245 336 199 0 0 332 247 88 148 60 62 57 36 551 535 1.213 .825 .592 .772 .631 3.578 80 410 .683 .53 100 5040 16190 29 39 327 337 0 490 235 255 .843 439 203 1.186 .606 -.246 -.724

Total number of rows: 11520

Table truncated, full table size 2573 Kbytes.




Supplementary data files not provided
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