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Sample GSM211785 Query DataSets for GSM211785
Status Public on Jul 20, 2007
Title J1501 KCl 0min vs 80min
Sample type RNA
 
Channel 1
Source name J1501 KCl 0min
Organism Streptomyces coelicolor
Characteristics J1501 KCl 0min
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name J1501 KCl 80min
Organism Streptomyces coelicolor
Characteristics J1501 KCl 80min
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1770, 15290; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.35; Parameter Scan Time = 09:41:15; Parameter PMT Volts = 730; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68415; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.35; Parameter Scan Time = 09:41:15; Parameter PMT Volts = 780; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68377; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri
Description Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46307.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 19, 2007
Last update date Jul 19, 2007
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)
GSE8530 The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation

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
1 884 958 650 680 234 278 729 820 684 731 79 140 0 0 392 461 315 373 31 35 16 16 512 219 .842 1.188 1.772 1.34 1.406 3.461 80 485 .731 .22 100 2090 15600 26 36 27 37 0 871 618 253 1.08 745 127 .926 1.611 .111 .688
2 1022 1077 633 687 389 390 874 960 670 729 241 273 0 0 525 641 345 361 36 42 19 21 779 514 .997 1.003 1.133 1.86 1.682 4.469 52 357 1.166 .4 90 2260 15600 26 35 44 53 0 979 625 355 .911 873 248 1.097 1.03 -.134 .042
3 1090 1180 673 721 417 459 892 964 706 772 219 243 0 0 505 637 212 278 50 43 40 37 876 462 .908 1.101 1.11 1.027 1.068 3.061 32 210 1.731 .42 70 2420 15580 25 32 61 68 -100 1073 655 417 1.001 876 221 .999 1.009 .001 .013
4 1344 1617 659 703 685 914 1481 1697 676 732 822 994 0 0 641 663 145 251 78 81 68 71 1599 1816 .749 1.334 1.209 1.222 1.083 2.552 32 220 1.147 .58 70 2550 15590 26 33 74 81 -100 1470 639 831 1.213 1543 904 .824 1.099 .279 .137
5 1052 1050 646 675 406 375 1095 1048 642 689 449 373 0 0 321 392 122 214 81 65 59 40 781 822 1.083 .924 .831 .938 .988 2.887 32 171 .982 .49 60 2730 15610 29 35 93 99 -100 955 614 341 .84 953 339 1.191 .755 -.252 -.405
6 781 811 631 746 150 65 743 758 627 758 112 12 0 0 339 281 120 217 48 27 36 13 215 124 2.308 .433 .107 .973 .945 4.197 80 431 1.246 .23 100 2890 15600 26 36 107 117 -100 737 678 59 .394 689 11 2.538 .097 -1.344 -3.36
7 1635 1381 651 714 984 667 1667 1326 691 749 1016 612 0 0 531 426 228 222 87 87 81 71 1651 1628 1.475 .678 .602 .574 .68 1.883 32 192 .671 .66 70 3020 15580 25 32 121 128 -100 1255 649 606 .616 1205 556 1.623 .548 -.698 -.869
8 1118 1321 667 734 451 587 1096 1377 688 757 429 643 0 0 473 578 173 219 67 65 63 61 1038 1072 .768 1.302 1.499 1.244 1.218 3.905 52 320 1.496 .54 80 3190 15580 25 33 138 146 -100 1201 667 534 1.183 1252 585 .845 1.363 .243 .446
9 1010 1044 659 699 351 345 1110 1065 687 723 451 366 0 0 354 128 214 238 66 66 58 16 696 817 1.017 .983 .812 .873 .771 1.964 12 98 .556 .43 50 3370 15590 27 32 157 162 -100 949 635 314 .894 968 333 1.119 .738 -.162 -.439
10 597 588 623 723 -26 -135 540 550 637 736 -83 -173 0 0 293 231 147 201 22 11 12 3 -161 -256 null null null 1.013 .976 3.545 80 462 1.972 .24 100 3530 15590 25 35 171 181 -100 535 657 -123 null 500 -157 null null null null
11 1661 1541 569 697 1092 844 1624 1636 588 709 1055 939 0 0 748 627 151 200 90 78 81 75 1936 1994 1.294 .773 .89 .733 .927 2.644 32 170 .73 .65 60 3690 15590 27 33 189 195 -100 1401 634 767 .703 1487 854 1.423 .809 -.509 -.306
12 863 906 629 715 234 191 730 734 778 908 101 19 0 0 513 446 1558 2059 0 0 0 0 425 120 1.225 .816 .188 .843 .976 3.289 80 483 .683 .36 100 3860 15590 25 35 204 214 -50 824 650 174 .742 667 17 1.348 .171 -.43 -2.548
13 3455 3081 533 620 2922 2461 3592 3159 717 1103 3059 2539 0 0 1688 1417 1594 3505 78 25 50 0 5383 5598 1.187 .842 .83 .79 .864 2.088 32 164 .795 .8 60 4010 15590 27 33 221 227 -100 2801 564 2237 .766 2872 2308 1.306 .755 -.385 -.406
14 984 1042 634 730 350 312 865 891 643 750 231 161 0 0 533 506 126 211 56 46 48 36 662 392 1.122 .891 .697 .769 .86 4.011 80 416 1.099 .55 100 4180 15590 25 35 236 246 -50 947 664 284 .81 810 146 1.234 .634 -.303 -.658
15 1111 1481 640 745 471 736 816 1196 656 774 176 451 0 0 684 931 144 244 51 56 46 48 1207 627 .64 1.563 2.563 1.62 1.705 3.475 80 393 1.718 .71 100 4340 15590 25 35 252 262 -50 1346 677 669 1.421 1087 410 .704 2.33 .506 1.22
16 809 965 632 690 177 275 630 695 640 713 -2 5 0 0 503 625 145 199 41 41 37 28 452 3 .644 1.554 null .797 .929 3.429 80 382 1.56 .58 100 4510 15590 25 35 269 279 -50 877 627 250 1.412 632 5 .708 null .498 null
17 1321 1356 615 721 706 635 1298 1246 626 737 683 525 0 0 659 616 130 188 76 75 71 59 1341 1208 1.112 .899 .769 .883 .869 3.07 52 259 .887 .7 80 4650 15580 25 33 284 292 0 1233 655 577 .818 1133 477 1.223 .699 -.29 -.517
18 927 939 627 703 300 236 822 780 630 707 195 77 0 0 500 452 118 192 56 38 46 32 536 272 1.271 .787 .395 .815 1.059 3.389 80 414 .997 .58 100 4830 15590 25 35 301 311 -50 854 639 215 .715 709 70 1.398 .359 -.484 -1.478
19 835 993 626 711 209 282 695 902 629 732 69 191 0 0 432 501 111 211 47 47 40 32 491 260 .741 1.349 2.768 1.207 1.263 3.235 80 378 1.668 .52 100 4990 15590 25 35 317 327 -50 903 646 256 1.227 820 174 .815 2.516 .295 1.331
20 870 880 612 727 258 153 661 790 614 730 49 63 0 0 519 406 124 200 47 35 43 23 411 112 1.686 .593 1.286 .771 .788 2.726 80 404 .807 .51 100 5150 15590 25 35 333 343 -50 800 661 139 .539 718 57 1.855 1.169 -.891 .225

Total number of rows: 11520

Table truncated, full table size 2604 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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