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Sample GSM90732 Query DataSets for GSM90732
Status Public on Jan 06, 2006
Title 6' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. A1
Sample type RNA
 
Channel 1
Source name N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
Organism Escherichia coli
Characteristics N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif
Organism Escherichia coli
Characteristics N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/19884.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 Jan 05, 2006
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 GPL2821
Series (2)
GSE3978 mRNA Decay in E. Coli Degradosome Mutants and their Parental Strains
GSE4394 Global analysis of Escherichia coli RNA degradosome function

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
1 951 697 247 190 704 507 963 714 252 192 716 524 0 0 230 183 44 54 99 97 98 96 1211 1240 1.389 .72 .732 .719 .723 1.694 156 917 .711 .88 140 1610 25370 130 144 62 76 0 652 178 474 .674 668 490 1.484 .685 -.57 -.547
2 978 718 244 199 734 519 985 712 259 202 741 513 0 0 187 165 65 61 100 100 100 97 1253 1254 1.414 .707 .692 .686 .706 1.531 80 472 .694 .83 100 1820 25390 134 144 85 95 0 672 186 486 .661 666 480 1.512 .648 -.596 -.627
3 1109 832 247 189 862 643 1184 871 256 191 937 682 0 0 434 300 53 58 90 98 87 92 1505 1619 1.341 .746 .728 .8 .748 2.761 120 644 .704 .87 120 2050 25360 130 142 107 119 0 778 177 601 .698 815 638 1.433 .681 -.519 -.555
4 1019 611 239 177 780 434 1038 622 241 183 799 445 0 0 273 166 38 51 100 98 100 97 1214 1244 1.797 .556 .557 .546 .569 1.691 156 719 .522 .87 140 2250 25370 130 144 126 140 0 572 166 406 .52 582 416 1.921 .521 -.942 -.941
5 812 607 243 183 569 424 812 613 246 189 569 430 0 0 116 125 47 52 100 98 100 96 993 999 1.342 .745 .756 .722 .769 1.587 156 704 .733 .86 140 2460 25370 130 144 147 161 0 568 171 397 .697 573 402 1.435 .707 -.521 -.5
6 1168 696 255 191 913 505 1181 695 267 197 926 504 0 0 145 137 94 60 100 99 100 97 1418 1430 1.808 .553 .544 .526 .57 1.596 156 795 .524 .88 150 2660 25360 128 143 166 181 0 651 179 472 .517 650 471 1.933 .509 -.951 -.974
7 620 485 246 185 374 300 649 490 256 189 403 305 0 0 127 120 74 58 93 95 90 93 674 708 1.247 .802 .757 .835 .816 2.024 208 988 .778 .81 160 2880 25370 129 145 188 204 0 454 173 281 .75 458 285 1.333 .708 -.414 -.498
8 1189 719 218 173 971 546 1239 776 225 172 1021 603 0 0 305 243 49 48 100 96 100 93 1517 1624 1.778 .562 .591 .49 .598 2.623 32 176 .542 .8 60 3070 25350 132 138 212 218 0 673 162 511 .526 726 564 1.901 .552 -.927 -.856
9 767 597 236 184 531 413 748 604 243 187 512 420 0 0 150 149 103 52 99 99 99 96 944 932 1.286 .778 .82 .744 .797 1.563 156 950 .789 .87 150 3300 25360 128 143 230 245 0 558 172 386 .728 565 393 1.374 .767 -.459 -.382
10 1479 970 245 188 1234 782 1490 1011 251 192 1245 823 0 0 197 214 106 54 100 100 100 98 2016 2068 1.578 .634 .661 .604 .658 1.547 156 799 .625 .9 140 3510 25360 129 143 252 266 0 907 176 732 .593 946 770 1.687 .618 -.754 -.693
11 692 540 242 185 450 355 698 549 244 190 456 364 0 0 95 101 38 53 100 99 98 98 805 820 1.268 .789 .798 .791 .802 1.517 156 714 .761 .85 140 3710 25370 130 144 272 286 0 505 173 332 .738 514 341 1.355 .747 -.438 -.421
12 917 646 236 183 681 463 937 648 238 187 701 465 0 0 167 117 36 49 98 99 97 99 1144 1166 1.471 .68 .663 .707 .673 1.842 156 848 .631 .85 150 3930 25370 129 144 293 308 0 604 171 433 .636 606 435 1.572 .621 -.653 -.688
13 997 668 223 169 774 499 1031 698 224 169 808 529 0 0 303 180 33 45 100 100 100 100 1273 1337 1.551 .645 .655 .658 .586 1.531 32 236 .572 .79 70 4120 25350 131 138 316 323 0 625 158 467 .603 653 495 1.658 .612 -.73 -.707
14 2189 1140 236 183 1953 957 736 587 239 185 500 404 0 0 7954 2653 37 49 97 98 96 95 2910 904 2.041 .49 .808 .785 .826 2.037 208 958 .274 .77 160 4350 25370 129 145 335 351 0 1066 171 895 .458 549 378 2.182 .756 -1.125 -.404
15 662 515 235 184 427 331 644 507 239 187 409 323 0 0 123 96 40 53 100 100 99 100 758 732 1.29 .775 .79 .777 .737 1.484 120 652 .718 .83 130 4540 25370 130 143 355 368 0 482 172 310 .725 474 302 1.379 .739 -.464 -.437
16 1249 757 226 175 1023 582 1226 781 225 177 1000 606 0 0 532 308 33 48 100 96 100 96 1605 1606 1.758 .569 .606 .548 .523 2.71 32 236 .539 .81 70 4760 25340 130 137 380 387 0 708 164 544 .532 731 567 1.879 .567 -.91 -.819
17 767 608 236 181 531 427 828 655 238 184 592 474 0 0 237 204 36 49 92 94 89 90 958 1066 1.244 .804 .801 .857 .832 2.399 156 911 .807 .86 140 4970 25360 129 143 398 412 0 569 169 399 .752 613 443 1.329 .749 -.411 -.417
18 1018 653 231 180 787 473 1020 662 233 183 789 482 0 0 289 232 35 49 98 94 98 90 1260 1271 1.664 .601 .611 .552 .602 2.039 120 630 .613 .88 120 5180 25350 129 141 420 432 0 611 168 442 .562 619 451 1.779 .571 -.831 -.807
19 707 536 234 180 473 356 712 556 237 183 478 376 0 0 115 133 34 49 99 96 99 94 829 854 1.329 .753 .787 .697 .796 1.988 156 844 .788 .83 150 5390 25350 127 142 439 454 0 501 168 333 .704 520 352 1.42 .736 -.506 -.443
20 1060 727 242 184 818 543 1067 740 243 185 825 556 0 0 149 166 35 49 100 99 99 95 1361 1381 1.506 .664 .674 .624 .676 1.831 156 882 .661 .87 140 5600 25350 128 142 461 475 0 680 172 508 .621 692 520 1.61 .63 -.687 -.666

Total number of rows: 6144

Table truncated, full table size 1353 Kbytes.




Supplementary data files not provided
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