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Sample GSM63788 Query DataSets for GSM63788
Status Public on Jul 12, 2005
Title Heat shock 37C SMM 15 min 0403
Sample type RNA
 
Channel 1
Source name time zero OD 5
Organism Streptomyces coelicolor
Characteristics time zero OD 5
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 15 min
Organism Streptomyces coelicolor
Characteristics 15 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50494.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
1 531 586 376 330 155 256 474 481 382 348 98 151 0 0 220 415 75 147 56 51 37 27 411 249 .605 1.652 1.541 1.735 1.445 3.997 80 444 3.174 .203 100 2420 15300 40 50 31 41 -100 715 402 312 2.014 587 184 .496 1.879 1.01 .91
2 530 582 382 329 148 253 494 427 385 331 112 98 0 0 188 423 75 125 60 42 40 31 401 210 .585 1.709 .875 1.623 1.203 4.529 80 387 5.151 .126 100 2580 15300 40 50 47 57 -100 710 401 309 2.085 521 120 .48 1.067 1.06 .094
3 550 625 384 331 166 294 490 444 385 347 106 113 0 0 219 457 77 138 62 47 40 31 460 219 .565 1.771 1.066 1.167 1.411 3.597 80 368 3.473 .222 100 2740 15300 40 50 63 73 -100 762 404 359 2.16 541 138 .463 1.3 1.111 .379
4 1440 1664 374 315 1066 1349 1175 1471 382 333 801 1156 0 0 1109 1176 97 136 78 82 75 75 2415 1957 .79 1.265 1.443 1.071 .997 3.161 52 325 1.186 .488 90 2890 15300 40 49 78 87 0 2029 384 1645 1.543 1794 1410 .648 1.76 .626 .816
5 625 454 373 306 252 148 445 389 387 362 72 83 0 0 463 254 148 762 42 1 37 0 400 155 1.703 .587 1.153 .601 .497 3.437 80 410 .455 .266 100 3060 15300 40 50 95 105 -100 554 373 180 .716 474 101 1.396 1.406 -.482 .491
6 510 485 386 308 124 177 373 397 383 328 -13 89 0 0 441 333 84 137 37 42 28 31 301 76 .701 1.427 null .933 .731 3.317 80 382 .806 .191 100 3220 15300 40 50 111 121 -100 591 376 216 1.741 484 109 .574 null .8 null
7 1605 1052 393 325 1212 727 1413 993 395 339 1020 668 0 0 1238 725 85 136 77 76 75 65 1939 1688 1.667 .6 .655 .524 .509 3.06 80 400 .465 .354 110 3390 15310 40 51 127 138 0 1283 396 887 .732 1211 815 1.367 .799 -.451 -.324
8 876 840 412 362 464 478 763 762 414 379 351 400 0 0 642 527 78 147 66 68 60 58 942 751 .971 1.03 1.14 .895 .896 2.389 80 446 1.05 .271 110 3540 15310 40 51 142 153 0 1024 441 583 1.256 929 488 .796 1.39 .329 .475
9 948 636 431 360 517 276 869 552 435 391 438 192 0 0 444 319 79 200 81 46 75 34 793 630 1.873 .534 .438 .461 .501 4.403 32 176 .266 .063 60 3710 15300 42 48 162 168 0 776 439 337 .651 673 234 1.536 .535 -.619 -.904
10 553 413 420 402 133 11 436 374 431 475 16 -28 0 0 381 235 110 1105 37 0 28 0 144 -12 12.091 .083 null .892 .77 4.367 80 430 119.873 .002 100 3870 15300 40 50 176 186 -50 504 490 13 .101 456 -34 9.915 null -3.31 null
11 2130 2024 396 367 1734 1657 1692 1673 429 431 1296 1306 0 0 1545 1466 442 428 75 71 63 65 3391 2602 1.046 .956 1.008 .951 .939 2.816 52 274 .96 .652 80 4030 15300 41 49 193 201 0 2468 448 2021 1.165 2040 1593 .858 1.229 .221 .297
12 1529 1071 390 359 1139 712 1349 901 391 381 959 542 0 0 975 634 82 274 84 76 80 50 1851 1501 1.6 .625 .565 .518 .634 2.843 52 336 .54 .431 90 4180 15290 39 48 207 216 0 1306 438 868 .762 1099 661 1.312 .689 -.392 -.537
13 1684 3342 364 337 1320 3005 1064 2295 373 352 700 1958 0 0 1428 2746 100 146 80 92 73 92 4325 2658 .439 2.277 2.797 2.648 2.556 3.035 52 293 2.63 .468 80 4340 15290 40 48 224 232 0 4076 411 3665 2.776 2799 2388 .36 3.411 1.473 1.77
14 1325 1087 402 399 923 688 1347 1117 406 411 945 718 0 0 721 452 99 162 81 85 75 78 1611 1663 1.342 .745 .76 .731 .629 2.296 80 480 .633 .458 110 4510 15300 39 50 239 250 0 1326 487 839 .909 1362 876 1.1 .927 -.138 -.11
15 1240 1052 420 435 820 617 1245 942 438 443 825 507 0 0 682 584 231 163 76 73 63 63 1437 1332 1.329 .752 .615 .87 .787 3.358 52 293 .791 .467 80 4670 15290 40 48 257 265 0 1283 530 752 .918 1149 618 1.09 .749 -.124 -.416
16 936 965 384 352 552 613 759 809 416 396 375 457 0 0 561 596 275 342 62 56 40 40 1165 832 .9 1.111 1.219 1.382 1.321 2.606 32 230 1.217 .281 70 4830 15290 40 47 273 280 0 1177 429 748 1.354 987 557 .738 1.486 .438 .572
17 2040 1229 397 367 1643 862 1762 910 459 387 1365 543 0 0 1715 1253 300 193 84 75 81 59 2505 1908 1.906 .525 .398 .568 .624 2.326 32 230 .531 .414 70 4980 15290 40 47 288 295 0 1499 448 1051 .64 1110 662 1.563 .485 -.644 -1.044
18 343 332 425 390 -82 -58 107 226 460 427 -318 -164 0 0 497 293 254 224 12 18 8 6 -140 -482 null null null .829 .807 3.299 80 458 1.244 .042 100 5160 15290 39 49 305 315 -50 405 476 -71 null 276 -200 null null null null
19 1431 1197 419 396 1012 801 1286 1203 424 398 867 807 0 0 868 625 106 158 81 90 81 81 1813 1674 1.263 .792 .931 .807 .678 2.993 32 218 .677 .488 70 5310 15290 40 47 321 328 0 1460 483 977 .965 1467 984 1.036 1.135 -.051 .183
20 1162 1092 406 373 756 719 1205 1086 413 407 799 713 0 0 666 585 111 499 78 53 75 34 1475 1512 1.051 .951 .892 .665 .782 2.988 32 232 2.61 .151 70 5470 15300 41 48 337 344 0 1332 455 877 1.16 1324 870 .862 1.088 .214 .122

Total number of rows: 11520

Table truncated, full table size 2625 Kbytes.




Supplementary data files not provided
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