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Sample GSM63761 Query DataSets for GSM63761
Status Public on Jul 12, 2005
Title M600 R5 OD 1 (10hr) vs 45 hr
Sample type RNA
 
Channel 1
Source name OD 1 ~10 hr
Organism Streptomyces coelicolor
Characteristics OD 1 ~10 hr
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 45 hr
Organism Streptomyces coelicolor
Characteristics 45 hr
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49651.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jul 11, 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 (1)
GSE2921 Regional organization of gene expression in Streptomyces coelicolor

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
1 498 486 350 240 148 246 464 447 369 265 114 207 0 0 149 253 98 126 55 65 33 41 394 321 .602 1.662 1.816 1.64 1.597 2.756 80 428 2.009 .35 100 2070 15610 20 30 8 18 -100 451 223 228 1.543 415 192 .648 1.686 .626 .753
2 554 470 364 240 190 230 488 436 376 249 124 196 0 0 239 266 88 102 60 65 40 47 420 320 .826 1.211 1.581 1.216 1.178 3.335 80 392 1.25 .32 100 2230 15610 20 30 24 34 -100 436 223 214 1.124 405 182 .89 1.467 .168 .553
3 532 515 357 237 175 278 453 456 372 244 96 219 0 0 231 300 98 100 50 65 33 52 453 315 .629 1.589 2.281 1.75 1.873 3.388 80 379 1.611 .394 100 2390 15610 20 30 40 50 -100 478 220 258 1.475 423 203 .678 2.118 .56 1.083
4 1164 975 319 209 845 766 972 772 332 226 653 563 0 0 799 652 85 91 81 91 75 85 1611 1216 1.103 .907 .862 .94 .861 2.44 80 411 .845 .738 100 2540 15620 21 31 55 65 0 905 194 711 .842 717 523 1.188 .8 -.249 -.321
5 431 400 312 208 119 192 330 300 326 224 18 92 0 0 359 274 83 93 33 48 27 35 311 110 .62 1.613 5.111 .959 .742 3.033 80 404 .852 .37 100 2720 15610 20 30 73 83 -100 371 193 178 1.498 278 85 .668 4.745 .583 2.246
6 417 334 313 215 104 119 286 261 323 225 -27 46 0 0 374 215 77 91 37 35 25 25 223 19 .874 1.144 null .557 .466 4.551 80 382 .499 .274 100 2880 15610 20 30 89 99 -100 310 200 110 1.062 242 43 .941 null .087 null
7 771 979 317 212 454 767 596 820 328 228 279 608 0 0 508 615 83 104 69 86 61 78 1221 887 .592 1.689 2.179 1.506 1.598 2.844 52 267 1.568 .518 80 3020 15610 21 29 104 112 0 909 197 712 1.568 761 564 .638 2.023 .649 1.017
8 888 1516 329 276 559 1240 959 1413 353 333 630 1137 0 0 488 538 135 237 66 100 66 91 1799 1767 .451 2.218 1.805 2.878 1.914 2.763 12 104 1.967 .552 50 3190 15610 22 27 122 127 0 1407 256 1151 2.059 1312 1056 .486 1.675 1.042 .745
9 869 755 325 252 544 503 929 741 341 260 604 489 0 0 397 287 85 100 83 91 66 91 1047 1093 1.082 .925 .81 1.132 .987 2.514 12 104 .869 .487 50 3360 15610 22 27 139 144 0 701 234 467 .858 688 454 1.165 .752 -.22 -.412
10 1104 621 313 202 791 419 1033 593 313 209 720 391 0 0 584 314 86 92 100 91 100 58 1210 1111 1.888 .53 .543 .534 .423 2.239 12 68 .416 .483 40 3510 15620 24 28 155 159 0 576 188 389 .492 550 363 2.034 .504 -1.024 -.988
11 1936 1391 311 198 1625 1193 2062 1395 322 217 1751 1197 0 0 1230 805 75 93 87 90 84 84 2818 2948 1.362 .734 .684 .715 .581 4.121 32 172 .635 .642 60 3670 15620 23 29 170 176 0 1291 184 1107 .682 1295 1111 1.467 .635 -.553 -.656
12 750 895 309 214 441 681 650 809 316 225 341 595 0 0 484 559 75 98 76 88 68 81 1122 936 .648 1.544 1.745 1.435 1.398 3.449 80 464 1.466 .457 100 3850 15600 19 29 186 196 0 831 199 632 1.434 751 552 .698 1.62 .52 .696
13 2373 2557 303 203 2070 2354 1181 1052 315 222 878 849 0 0 2525 2594 99 103 68 93 65 87 4424 1727 .879 1.137 .967 1.152 .791 4.274 32 160 1.106 .552 60 4020 15600 21 27 205 211 0 2374 188 2185 1.056 977 788 .947 .898 .078 -.156
14 785 841 315 226 470 615 754 736 325 237 439 510 0 0 413 507 87 91 82 87 76 80 1085 949 .764 1.309 1.162 .893 1.052 3.56 80 504 1.343 .534 110 4180 15600 18 29 218 229 0 781 210 571 1.215 683 473 .823 1.078 .281 .109
15 1249 1463 361 267 888 1196 1374 1513 408 380 1013 1246 0 0 564 374 188 505 83 91 75 75 2084 2259 .742 1.347 1.23 1.479 1.153 2.315 12 104 1.002 .512 50 4330 15600 21 26 236 241 0 1358 248 1110 1.25 1405 1157 .8 1.142 .322 .191
16 161 244 296 228 -135 16 123 202 334 299 -173 -26 0 0 101 157 235 470 1 1 0 0 -119 -199 null null null .519 .546 2.281 80 443 3.325 .237 100 4490 15600 19 29 250 260 -50 227 212 15 null 188 -24 null null null null
17 1135 1446 336 256 799 1190 1095 1595 389 300 759 1339 0 0 619 879 251 149 83 83 83 83 1989 2098 .671 1.489 1.764 1.344 1.38 6.911 12 68 1.922 .174 40 4630 15610 23 27 267 271 0 1342 238 1105 1.383 1481 1243 .723 1.638 .467 .712
18 838 958 328 235 510 723 971 961 358 310 643 726 0 0 574 528 150 274 65 75 62 62 1233 1369 .705 1.418 1.129 .927 .973 1.936 32 158 .925 .375 60 4830 15600 21 27 286 292 0 889 218 671 1.316 892 674 .76 1.048 .396 .068
19 511 541 324 235 187 306 426 443 340 259 102 208 0 0 350 326 97 131 50 63 30 43 493 310 .611 1.636 2.039 1.298 1.193 3.261 120 540 1.165 .373 120 4980 15590 17 29 298 310 0 502 218 284 1.519 411 193 .658 1.893 .603 .921
20 980 1242 326 235 654 1007 900 1167 352 268 574 932 0 0 598 700 125 168 75 93 71 84 1661 1506 .649 1.54 1.624 1.687 1.422 3.035 32 189 1.392 .452 70 5110 15600 20 27 313 320 0 1153 218 935 1.429 1083 865 .7 1.507 .515 .592

Total number of rows: 11520

Table truncated, full table size 2552 Kbytes.




Supplementary data files not provided
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