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Sample GSM63752 Query DataSets for GSM63752
Status Public on Jul 12, 2005
Title M600 R5 OD 1 (10hr) vs 34 hr
Sample type RNA
 
Channel 1
Source name M600 R5 OD 1 (10hr)
Organism Streptomyces coelicolor
Characteristics M600 R5 OD 1 (10hr)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 34 hr
Organism Streptomyces coelicolor
Characteristics 34 hr
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49685.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
1 519 735 321 520 198 215 385 618 331 538 64 98 0 0 522 532 83 168 42 30 21 21 413 162 .921 1.086 1.531 1.915 2.211 4.818 80 423 1.347 .283 100 2150 15680 14 24 32 42 -100 709 502 207 1.048 596 95 .955 1.477 .067 .563
2 399 682 311 478 88 204 370 621 315 489 59 143 0 0 164 244 69 129 42 55 20 31 292 202 .431 2.318 2.424 2.072 2.311 3.98 80 386 8.273 .022 100 2320 15680 14 24 49 59 -100 658 461 197 2.236 599 138 .447 2.338 1.161 1.225
3 658 981 322 482 336 499 381 682 330 490 59 200 0 0 873 973 79 127 40 55 25 46 835 259 .673 1.485 3.39 2.424 3.062 3.797 80 394 1.216 .573 100 2480 15680 14 24 65 75 -100 946 465 481 1.433 658 193 .698 3.27 .519 1.709
4 2620 1722 344 509 2276 1213 1795 1443 378 529 1451 934 0 0 2088 1321 174 198 81 75 78 62 3489 2385 1.876 .533 .644 .666 .566 2.657 32 196 .49 .456 70 2600 15680 15 22 78 85 0 1661 491 1170 .514 1392 901 1.945 .621 -.96 -.687
5 426 574 324 496 102 78 289 467 341 508 -35 -29 0 0 503 465 124 148 20 26 13 16 180 -64 1.308 .765 null 1.534 1.691 3.593 80 431 1.012 .301 100 2800 15680 14 24 97 107 -100 554 479 75 .738 451 -28 1.355 null -.439 null
6 516 591 305 469 211 122 375 526 312 477 70 57 0 0 476 284 67 132 51 33 36 20 333 127 1.73 .578 .814 .782 .634 3.235 80 370 .476 .155 100 2960 15680 14 24 113 123 -100 570 452 118 .558 507 55 1.793 .786 -.842 -.348
7 1099 1452 318 501 781 951 679 1141 343 517 361 640 0 0 1021 1276 146 147 69 61 55 55 1732 1001 .821 1.218 1.773 1.582 1.629 3.155 52 249 1.41 .442 80 3070 15680 15 23 125 133 0 1401 483 917 1.175 1101 617 .851 1.71 .232 .774
8 1293 2068 355 618 938 1450 1111 2147 424 680 756 1529 0 0 835 916 384 417 66 83 50 75 2388 2285 .647 1.546 2.022 1.731 1.523 2.002 12 104 1.273 .442 50 3240 15680 16 21 143 148 0 1995 596 1399 1.491 2071 1475 .671 1.951 .577 .964
9 884 1204 343 565 541 639 691 1296 362 598 348 731 0 0 592 777 122 210 68 62 65 62 1180 1079 .847 1.181 2.101 1.642 1.479 3.284 32 174 1.627 .242 60 3410 15690 17 23 160 166 0 1162 545 616 1.14 1250 705 .878 2.027 .188 1.019
10 1022 1016 334 555 688 461 1246 1213 332 574 912 658 0 0 729 568 150 224 66 66 58 58 1149 1570 1.492 .67 .721 .718 .822 1.893 12 62 .698 .213 40 3560 15680 17 21 176 180 0 980 535 445 .646 1170 635 1.547 .696 -.629 -.523
11 3959 2139 328 484 3631 1655 4471 2221 407 517 4143 1737 0 0 2571 889 369 206 83 100 75 100 5286 5880 2.194 .456 .419 .559 .474 3.227 12 104 .31 .562 50 3720 15680 16 21 191 196 0 2064 467 1597 .44 2143 1676 2.274 .404 -1.185 -1.306
12 1532 2083 335 513 1197 1570 1457 2284 379 577 1122 1771 0 0 1060 1219 269 290 71 84 62 65 2767 2893 .762 1.312 1.578 1.135 1.334 3.861 32 175 1.35 .398 60 3880 15690 17 23 207 213 0 2010 495 1515 1.265 2204 1709 .79 1.523 .34 .607
13 2035 1958 320 483 1715 1475 601 1004 336 510 281 521 0 0 3460 2354 158 203 61 71 46 58 3190 802 1.163 .86 1.854 1.29 1.43 4.506 80 461 .582 .346 110 4070 15690 14 25 223 234 0 1889 466 1423 .83 969 503 1.205 1.789 -.269 .839
14 1073 1578 339 548 734 1030 840 1260 350 550 501 712 0 0 821 1150 79 146 65 63 61 60 1764 1213 .713 1.403 1.421 2.018 1.622 4.855 80 407 1.863 .287 100 4220 15670 13 23 239 249 0 1522 529 994 1.354 1216 687 .739 1.371 .437 .455
15 2633 1699 414 650 2219 1049 2946 1866 465 716 2532 1216 0 0 952 1148 216 277 100 58 100 58 3268 3748 2.115 .473 .48 .511 .692 4.562 12 62 .689 .278 40 4380 15680 17 21 258 262 0 1639 627 1012 .456 1800 1173 2.193 .463 -1.133 -1.11
16 1007 2096 301 502 706 1594 523 1758 339 608 222 1256 0 0 1016 1853 223 468 50 65 31 56 2300 1478 .443 2.258 5.658 3.413 4.111 5.823 32 160 4.616 .104 60 4520 15670 15 21 271 277 0 2022 484 1538 2.178 1696 1212 .459 5.458 1.123 2.448
17 1183 1366 345 517 838 849 966 1163 378 575 621 646 0 0 876 852 187 328 75 68 61 48 1687 1267 .987 1.013 1.04 1.242 1.148 2.485 80 460 1.051 .454 100 4700 15680 14 24 287 297 0 1318 499 819 .977 1122 623 1.023 1.004 -.033 .005
18 1816 2930 335 568 1481 2362 2205 2847 393 691 1870 2279 0 0 917 526 259 377 83 100 75 100 3843 4149 .627 1.595 1.219 1.728 1.607 1.852 12 98 1.336 .44 50 4860 15670 15 20 305 310 0 2827 548 2279 1.539 2747 2199 .65 1.176 .622 .234
19 786 1343 349 543 437 800 724 1323 373 569 375 780 0 0 531 754 177 232 65 71 51 63 1237 1155 .546 1.831 2.08 1.549 1.584 3.053 80 535 2.031 .451 110 5030 15680 13 24 319 330 0 1296 524 772 1.766 1276 753 .566 2.007 .821 1.005
20 1679 2129 366 574 1313 1555 1999 2076 446 664 1633 1502 0 0 1004 350 360 415 75 100 58 100 2868 3135 .844 1.184 .92 1.202 .975 2.111 12 98 .752 .364 50 5200 15670 15 20 339 344 -100 2054 554 1500 1.143 2003 1449 .875 .887 .192 -.172

Total number of rows: 11520

Table truncated, full table size 2633 Kbytes.




Supplementary data files not provided
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