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Sample GSM65526 Query DataSets for GSM65526
Status Public on Jul 26, 2005
Title ATCC19609 R5NG 2/9/03 16 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 16 h
Organism Streptomyces coelicolor
Characteristics 16 h
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Strain comparison, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43929.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
1 582 703 296 234 286 469 475 529 301 256 179 295 0 0 319 575 76 158 65 59 56 46 755 474 .61 1.64 1.648 1.447 1.29 5.519 32 171 2.746 .51 60 2290 14920 33 39 34 40 -100 596 198 397 1.39 448 250 .72 1.397 .475 .482
2 535 660 282 222 253 438 449 437 286 250 167 215 0 0 306 544 74 163 56 56 53 40 691 382 .578 1.731 1.287 1.81 1.163 4.741 32 170 2.967 .45 60 2470 14920 33 39 52 58 -100 559 188 371 1.467 370 182 .682 1.091 .553 .126
3 595 1144 385 274 210 870 502 1215 429 372 117 941 0 0 292 692 170 325 50 66 16 58 1080 1058 .241 4.143 8.043 2.634 3.513 4.507 12 104 3.648 .36 50 2620 14930 34 39 67 72 -100 969 232 737 3.511 1030 797 .285 6.816 1.812 2.769
4 883 705 330 239 553 466 916 717 408 305 586 478 0 0 311 225 1017 632 7 21 0 0 1019 1064 1.187 .843 .816 .885 .865 2.075 80 451 .477 .62 100 2770 14910 30 40 80 90 0 597 203 395 .714 608 405 1.4 .691 -.486 -.533
5 672 429 316 230 356 199 659 409 318 237 343 179 0 0 180 133 89 90 93 84 90 50 555 522 1.789 .559 .522 .581 .506 2.448 32 170 .436 .45 60 2940 14910 32 38 99 105 0 364 195 169 .474 347 152 2.111 .442 -1.078 -1.177
6 713 536 303 227 410 309 681 475 304 236 378 248 0 0 264 235 84 92 92 82 80 67 719 626 1.327 .754 .656 .751 .671 2.844 52 284 .099 .23 80 3110 14900 30 38 115 123 0 454 192 262 .639 403 210 1.566 .556 -.647 -.847
7 1141 981 338 234 803 747 1147 948 399 249 809 714 0 0 396 335 782 93 55 100 2 97 1550 1523 1.075 .93 .883 .961 .885 2.001 80 395 .911 .78 100 3270 14910 30 40 130 140 0 831 198 633 .788 803 605 1.268 .748 -.343 -.419
8 842 764 327 256 515 508 872 803 422 264 545 547 0 0 278 265 926 96 0 94 0 86 1023 1092 1.014 .986 1.004 .909 .956 2.282 52 285 1.026 .74 80 3420 14910 31 39 146 154 0 647 217 431 .836 681 464 1.196 .851 -.259 -.234
9 802 551 281 243 521 308 802 524 287 250 521 281 0 0 253 186 70 91 96 87 93 75 829 802 1.692 .591 .539 .564 .608 2.604 32 236 .452 .52 70 3580 14910 31 38 162 169 0 467 206 261 .501 444 238 1.996 .457 -.997 -1.13
10 692 428 283 225 409 203 693 427 352 276 410 202 0 0 214 125 687 373 12 6 0 0 612 612 2.015 .496 .493 .534 .609 2.607 32 170 .383 .55 60 3750 14910 32 38 180 186 0 363 191 172 .421 362 171 2.377 .418 -1.249 -1.26
11 1186 1120 298 224 888 896 1163 1203 311 231 865 979 0 0 398 369 76 86 100 100 100 100 1784 1844 .991 1.009 1.132 1.026 1.03 1.618 52 385 .935 .82 90 3910 14910 30 39 194 203 0 949 190 759 .855 1019 830 1.169 .959 -.226 -.06
12 1201 1030 326 214 875 816 1200 1090 338 229 874 876 0 0 403 367 115 95 93 93 93 90 1691 1750 1.072 .933 1.002 .77 .862 2.203 32 236 .865 .77 70 4070 14910 31 38 211 218 0 873 181 692 .79 924 742 1.265 .849 -.34 -.235
13 896 750 273 197 623 553 907 782 274 209 634 585 0 0 349 255 69 85 96 93 90 93 1176 1219 1.127 .888 .923 .941 .972 2.153 32 231 .748 .7 70 4230 14910 31 38 227 234 0 636 167 469 .752 663 496 1.329 .782 -.411 -.355
14 1001 850 310 245 691 605 951 857 376 255 641 612 0 0 362 314 758 123 42 93 0 86 1296 1253 1.142 .876 .955 .792 .868 2.322 80 525 .884 .77 110 4390 14920 30 41 241 252 0 720 208 513 .742 726 519 1.348 .809 -.431 -.306
15 771 624 331 246 440 378 794 616 334 254 463 370 0 0 282 188 81 102 86 92 80 80 818 833 1.164 .859 .799 .78 .742 2.072 52 318 .765 .69 80 4550 14920 32 40 259 267 0 529 208 320 .728 522 314 1.374 .677 -.458 -.562
16 702 685 311 251 391 434 717 671 367 274 406 420 0 0 232 285 173 153 83 83 66 66 825 826 .901 1.11 1.034 1.27 1.148 3.081 12 98 .654 .42 50 4720 14910 32 37 277 282 0 581 213 368 .941 569 356 1.063 .877 -.088 -.19
17 979 894 300 220 679 674 1022 902 300 227 722 682 0 0 426 320 71 88 88 94 84 94 1353 1404 1.007 .993 .945 .985 .85 2.323 52 332 .947 .67 80 4870 14920 32 40 291 299 0 758 186 571 .841 764 578 1.189 .801 -.249 -.321
18 1101 1321 310 233 791 1088 1136 1265 337 261 826 1032 0 0 474 377 178 174 90 100 75 96 1879 1858 .727 1.375 1.249 1.558 1.363 2.063 32 236 1.261 .8 70 5030 14920 32 39 307 314 0 1119 197 922 1.166 1072 875 .858 1.059 .221 .082
19 767 574 341 243 426 331 795 542 372 255 454 299 0 0 206 135 163 100 90 100 81 84 757 753 1.287 .777 .659 .701 .624 1.556 32 176 .649 .67 60 5180 14920 33 39 323 329 0 486 206 281 .658 459 253 1.519 .558 -.603 -.841
20 854 805 343 254 511 551 861 779 366 271 518 525 0 0 243 250 143 115 93 100 75 90 1062 1043 .927 1.078 1.014 1.152 1.051 2.57 32 232 1.048 .63 70 5320 14930 33 40 336 343 0 682 215 467 .914 660 445 1.094 .859 -.13 -.219

Total number of rows: 11520

Table truncated, full table size 2597 Kbytes.




Supplementary data files not provided
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