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Sample GSM65533 Query DataSets for GSM65533
Status Public on Jul 26, 2005
Title RUS R5NG 2/9/03 48 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 48 h
Organism Streptomyces coelicolor
Characteristics 48 h
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Strain comparison, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43941.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
1 672 1223 267 408 405 815 447 701 276 426 180 293 0 0 483 1127 75 115 65 75 53 61 1220 473 .497 2.012 1.628 2.349 2.579 4.377 52 313 2.84 .67 90 2020 15720 27 36 29 38 -100 1486 496 990 2.445 852 356 .409 1.978 1.29 .984
2 739 1226 284 452 455 774 497 1159 317 563 213 707 0 0 551 913 197 512 53 53 40 34 1229 920 .588 1.701 3.319 1.287 1.374 4.378 32 167 2.042 .72 60 2180 15730 30 36 47 53 -100 1490 549 941 2.067 1408 859 .484 4.033 1.048 2.012
3 713 1333 288 437 425 896 390 1057 293 453 102 620 0 0 582 967 73 153 57 65 46 61 1321 722 .474 2.108 6.078 2.272 2.018 4.754 52 301 2.635 .54 80 2340 15710 27 35 62 70 -100 1620 531 1089 2.562 1284 753 .39 7.386 1.357 2.885
4 888 699 271 412 617 287 908 666 292 432 637 254 0 0 289 202 179 155 94 71 76 46 904 891 2.15 .465 .399 .437 .498 2.351 52 371 .564 .65 90 2500 15710 26 35 77 86 0 849 501 349 .565 809 309 1.769 .485 -.823 -1.045
5 360 432 252 386 108 46 299 406 259 399 47 20 0 0 217 147 76 114 40 25 25 11 154 67 2.348 .426 .426 1.178 1.252 4.532 80 436 .552 .32 100 2700 15710 26 36 97 107 -50 525 469 56 .518 493 24 1.932 .517 -.95 -.952
6 355 463 248 373 107 90 303 438 254 382 55 65 0 0 188 195 66 105 47 38 27 21 197 120 1.189 .841 1.182 1.148 1.024 3.292 80 329 1.037 .54 100 2860 15700 25 35 113 123 -50 563 453 109 1.022 532 79 .978 1.436 .032 .522
7 917 896 272 406 645 490 930 953 280 428 658 547 0 0 390 309 76 159 91 83 87 70 1135 1205 1.316 .76 .831 .775 .756 2.268 80 402 .723 .77 100 2980 15700 25 35 125 135 0 1089 493 595 .923 1158 665 1.083 1.01 -.115 .015
8 679 641 271 428 408 213 696 621 276 437 425 193 0 0 359 300 62 121 75 57 71 44 621 618 1.915 .522 .454 .643 .645 3.757 52 373 .64 .58 90 3150 15700 25 34 142 151 0 779 520 259 .634 755 235 1.576 .552 -.657 -.858
9 597 636 310 446 287 190 582 580 359 454 272 134 0 0 200 163 166 149 75 33 33 33 477 406 1.511 .662 .493 .87 .829 3.697 12 68 .638 .28 40 3290 15710 29 33 159 163 0 773 542 231 .804 705 163 1.243 .599 -.314 -.74
10 316 387 252 407 64 -20 258 390 262 419 6 -17 0 0 170 136 84 139 27 7 25 5 44 -11 null null null .936 1.015 4.047 80 462 .849 .36 100 3510 15700 25 35 178 188 -50 470 495 -24 null 474 -21 null null null null
11 1237 1253 225 386 1012 867 1402 1280 241 407 1177 894 0 0 510 512 88 139 90 90 90 81 1879 2071 1.167 .857 .76 .902 .844 2.577 32 156 1 .74 60 3640 15710 28 34 193 199 0 1523 469 1054 1.041 1555 1086 .961 .923 .058 -.116
12 1098 1053 246 396 852 657 1168 1059 253 400 922 663 0 0 575 464 70 96 82 86 80 84 1509 1585 1.297 .771 .719 .773 .783 2.298 52 309 .751 .78 80 3790 15710 27 35 207 215 0 1280 481 798 .937 1287 806 1.067 .874 -.094 -.195
13 1152 1003 206 323 946 680 998 1033 233 346 792 710 0 0 430 232 116 117 100 100 100 100 1626 1502 1.391 .719 .896 .742 .708 1.587 12 68 .7 .74 40 3950 15710 29 33 225 229 0 1219 392 826 .873 1255 863 1.145 1.089 -.195 .123
14 879 888 279 436 600 452 870 897 301 445 591 461 0 0 377 321 156 119 88 82 75 67 1052 1052 1.327 .753 .78 .707 .804 2.183 80 485 .79 .78 100 4110 15700 25 35 238 248 0 1079 530 549 .915 1090 560 1.092 .948 -.128 -.077
15 880 865 320 471 560 394 790 911 370 493 470 440 0 0 225 142 169 139 100 91 100 83 954 910 1.421 .704 .936 .668 .751 1.712 12 68 .634 .75 40 4280 15710 29 33 258 262 0 1051 572 479 .855 1107 535 1.17 1.138 -.226 .186
16 598 693 210 324 388 369 600 710 215 333 390 386 0 0 278 264 66 103 88 90 75 73 757 776 1.051 .951 .99 1.031 .936 2.299 52 318 1.173 .63 80 4440 15710 27 35 272 280 0 842 394 448 1.156 863 469 .865 1.203 .209 .266
17 888 998 229 350 659 648 890 1039 242 366 661 689 0 0 407 390 83 106 92 92 86 82 1307 1350 1.017 .983 1.042 1.051 .917 2.55 52 369 .96 .77 90 4600 15690 24 33 287 296 0 1213 425 787 1.195 1263 837 .837 1.267 .257 .341
18 1261 1122 242 369 1019 753 1165 1187 297 414 923 818 0 0 355 310 227 159 100 91 100 91 1772 1741 1.353 .739 .886 .67 .773 2.094 12 104 .603 .75 50 4750 15700 27 32 304 309 0 1363 448 915 .898 1442 994 1.114 1.077 -.155 .107
19 798 837 250 407 548 430 777 839 273 420 527 432 0 0 154 190 106 150 100 100 100 75 978 959 1.274 .785 .82 .736 .646 1.719 12 104 .995 .73 50 4930 15700 27 32 322 327 0 1017 495 523 .953 1020 525 1.049 .996 -.069 -.006
20 808 843 249 384 559 459 758 801 259 382 509 417 0 0 418 283 74 94 84 93 81 90 1018 926 1.218 .821 .819 .81 .827 2.03 32 236 .741 .68 70 5080 15690 25 32 336 343 0 1024 467 558 .998 973 507 1.002 .996 -.003 -.006

Total number of rows: 11520

Table truncated, full table size 2611 Kbytes.




Supplementary data files not provided
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