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Sample GSM211787 Query DataSets for GSM211787
Status Public on Jul 20, 2007
Title sigB KCl 0min vs 80 min
Sample type RNA
 
Channel 1
Source name sigB KCl 0min
Organism Streptomyces coelicolor
Characteristics sigB KCl 0min
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name sigB KCl 80min
Organism Streptomyces coelicolor
Characteristics sigB 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 = 2000, 15410; 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 = 38.75; Parameter Scan Time = 10:11:52; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71667; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.14; 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 = 38.75; Parameter Scan Time = 10:11:52; Parameter PMT Volts = 780; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71629; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.96; 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/2003-12/47420.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
1 844 1234 453 476 391 758 702 1105 467 479 249 629 0 0 384 663 125 174 68 71 50 62 1149 878 .516 1.939 2.526 2.03 1.731 2.596 32 176 2.757 .56 60 2310 15680 24 30 28 34 -100 651 251 400 1.023 583 332 .978 1.333 .032 .414
2 921 1241 472 461 449 780 817 1151 470 468 345 690 0 0 411 740 89 134 84 68 71 65 1229 1035 .576 1.737 2 1.654 1.757 2.976 32 176 2.37 .65 60 2460 15660 22 28 43 49 -100 655 243 411 .916 607 364 1.091 1.055 -.126 .077
3 1152 1358 472 475 680 883 977 1279 507 532 505 804 0 0 932 635 164 234 78 87 59 68 1563 1309 .77 1.299 1.592 1.511 1.342 3.593 32 176 .934 .39 60 2630 15650 21 27 60 66 -100 716 251 466 .685 675 424 1.46 .84 -.546 -.252
4 1501 2659 508 510 993 2149 1785 2790 562 658 1277 2280 0 0 947 416 347 456 75 100 58 100 3142 3557 .462 2.164 1.785 1.733 1.388 1.651 12 104 1.472 .67 50 2780 15660 22 27 75 80 -100 1403 269 1134 1.142 1472 1203 .876 .942 .191 -.086
5 559 628 471 447 88 181 527 520 503 489 56 73 0 0 412 411 202 253 22 33 17 22 269 129 .486 2.057 1.304 1.089 1.055 2.995 80 448 1.296 .29 100 2960 15660 20 30 91 101 -50 331 236 95 1.085 274 39 .922 .688 .118 -.54
6 499 450 473 450 26 0 464 386 484 472 -9 -64 0 0 380 273 115 195 32 26 23 8 26 -73 null null null 1.045 .842 3.87 80 425 .72 .22 100 3120 15660 20 30 107 117 -50 237 237 0 null 204 -34 null null null null
7 1711 2300 515 489 1196 1811 1848 2365 522 631 1333 1876 0 0 436 366 285 427 91 100 83 100 3007 3209 .66 1.514 1.407 1.668 1.474 1.718 12 104 1.618 .54 50 3260 15670 23 28 123 128 -100 1213 258 955 .799 1248 990 1.252 .742 -.324 -.43
8 1091 2947 529 613 562 2334 1231 3415 533 720 702 2802 0 0 516 1008 291 504 58 100 58 83 2896 3504 .241 4.153 3.991 5.052 3.069 2.784 12 104 3.546 .68 50 3420 15670 23 28 139 144 0 1555 323 1231 2.191 1802 1478 .456 2.106 1.132 1.074
9 735 852 507 519 228 333 657 780 512 546 150 261 0 0 556 716 95 186 51 51 50 38 561 411 .685 1.461 1.74 1.061 .936 3.554 52 306 3.676 .19 80 3610 15670 22 30 157 165 0 449 274 176 .771 411 138 1.298 .918 -.376 -.124
10 514 476 495 498 19 -22 490 387 500 524 -5 -111 0 0 324 290 100 165 31 26 23 12 -3 -116 null null null 1.187 .968 2.733 80 465 2.453 .14 100 3770 15660 20 30 172 182 -50 251 263 -12 null 204 -59 null null null null
11 2926 3611 502 448 2424 3163 3473 3551 568 552 2971 3103 0 0 1306 676 543 417 83 100 83 100 5587 6074 .766 1.305 1.044 1.308 1.064 1.463 12 104 .874 .65 50 3910 15670 23 28 188 193 0 1905 236 1669 .688 1873 1637 1.453 .551 -.539 -.86
12 735 912 485 471 250 441 646 754 522 525 161 283 0 0 602 689 275 294 43 50 28 31 691 444 .567 1.764 1.758 .935 1.068 4.309 80 503 1.773 .46 100 4090 15660 20 30 204 214 -50 481 248 233 .931 398 149 1.075 .927 -.104 -.109
13 1996 3010 469 455 1527 2555 1611 2859 648 729 1142 2404 0 0 1211 1680 693 843 75 83 41 58 4082 3546 .598 1.673 2.105 1.96 1.895 4.27 12 104 1.473 .69 50 4240 15670 23 28 221 226 0 1588 240 1348 .883 1508 1268 1.133 1.111 -.18 .151
14 982 1136 489 497 493 639 1061 1121 534 559 572 624 0 0 592 631 360 408 60 60 41 42 1132 1196 .772 1.296 1.091 1.064 1.08 3.028 80 530 1.264 .46 110 4410 15660 19 30 235 246 0 599 262 337 .684 591 329 1.462 .576 -.548 -.797
15 1019 3416 504 519 515 2897 951 2866 536 562 447 2347 0 0 620 2307 316 382 55 88 38 81 3412 2794 .178 5.625 5.251 3.795 4.649 4.084 80 408 6.061 .63 100 4570 15670 21 31 252 262 0 1802 274 1528 2.968 1512 1238 .337 2.77 1.569 1.47
16 721 1182 476 450 245 732 577 770 500 501 101 320 0 0 595 1025 256 372 30 47 22 32 977 421 .335 2.988 3.168 1.629 1.465 4.654 80 481 2.663 .59 100 4730 15660 20 30 268 278 -50 624 237 386 1.576 406 169 .634 1.671 .656 .741
17 1363 2543 594 610 769 1933 1434 2950 620 701 840 2340 0 0 646 888 251 396 75 91 66 91 2702 3180 .398 2.514 2.786 3.02 2.255 2.326 12 104 2.123 .56 50 4890 15660 22 27 286 291 0 1342 322 1020 1.326 1556 1234 .754 1.47 .407 .555
18 1048 1170 513 502 535 668 963 1090 534 550 450 588 0 0 570 607 154 250 72 72 62 58 1203 1038 .801 1.249 1.307 1.104 1.221 4.868 80 456 1.4 .52 100 5060 15670 21 31 301 311 0 617 265 352 .659 575 310 1.518 .689 -.602 -.537
19 822 951 521 514 301 437 811 961 536 547 290 447 0 0 388 445 155 208 65 71 48 57 738 737 .689 1.452 1.541 1.618 1.509 2.177 52 284 1.556 .41 80 5210 15680 23 31 317 325 0 502 271 231 .766 507 236 1.306 .813 -.385 -.298
20 837 980 488 462 349 518 560 841 512 504 72 379 0 0 817 679 158 234 44 57 38 46 867 451 .674 1.484 5.264 1.248 1.045 3.589 52 347 1.32 .27 90 5380 15670 21 30 333 342 0 517 244 273 .783 444 200 1.277 2.777 -.353 1.474

Total number of rows: 11520

Table truncated, full table size 2602 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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