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Sample GSM211788 Query DataSets for GSM211788
Status Public on Jul 20, 2007
Title J1501 KCl 0min vs sigB KCl 0min
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 sigB KCl 0min
Organism Streptomyces coelicolor
Characteristics sigB KCl 0min
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 = 1870, 15430; 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 = 39.05; Parameter Scan Time = 10:39:50; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71695; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.16; 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 = 39.05; Parameter Scan Time = 10:39:50; Parameter PMT Volts = 780; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71657; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.06; 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/2003-12/47415.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
1 907 1201 459 479 448 722 715 866 494 550 256 387 0 0 396 977 257 381 46 50 37 34 1170 643 .62 1.612 1.512 1.524 1.263 4.036 32 176 .766 .17 60 2150 15700 24 30 25 31 -100 1264 504 760 1.696 912 407 .589 1.591 .763 .67
2 584 706 443 456 141 250 517 622 470 518 74 166 0 0 236 345 147 328 33 32 16 12 391 240 .564 1.773 2.243 1.42 1.785 6.477 80 468 4.914 .19 100 2310 15690 21 31 39 49 -100 743 480 263 1.866 655 175 .536 2.361 .9 1.24
3 979 1145 527 594 452 551 1047 1134 565 746 520 540 0 0 290 366 218 700 75 25 58 0 1003 1060 .82 1.219 1.038 1.628 1.375 2.479 12 104 4.743 .18 50 2450 15670 21 26 55 60 -100 1205 625 580 1.283 1194 568 .779 1.093 .36 .128
4 1035 1253 469 444 566 809 1252 1312 497 510 783 868 0 0 481 474 200 272 71 81 62 75 1375 1651 .7 1.429 1.109 1.033 1.106 2.861 32 176 1.517 .35 60 2620 15690 23 29 72 78 -100 1319 467 852 1.505 1381 914 .665 1.167 .589 .223
5 529 402 458 458 71 -56 415 321 484 489 -43 -137 0 0 440 293 158 225 23 10 17 7 15 -180 null null null .876 .974 3.303 80 438 .697 .17 100 2790 15690 21 31 87 97 -100 423 482 -59 null 338 -144 null null null null
6 484 400 453 470 31 -70 480 386 496 545 27 -84 0 0 274 205 449 491 8 1 0 0 -39 -57 null null null .683 .702 4.007 80 442 .605 .09 100 2950 15690 21 31 103 113 -100 421 495 -74 null 406 -88 null null null null
7 1517 1040 507 485 1010 555 1529 1085 573 570 1022 600 0 0 141 254 281 387 100 66 100 25 1565 1622 1.82 .55 .587 .47 .634 2.112 12 104 .671 .38 50 3110 15700 24 29 121 126 -100 1095 511 584 .578 1142 632 1.729 .618 -.79 -.694
8 1118 1563 465 516 653 1047 1224 1679 510 564 759 1163 0 0 393 551 230 233 87 90 81 87 1700 1922 .624 1.603 1.532 1.368 1.511 1.541 32 170 1.879 .57 60 3280 15700 24 30 138 144 -100 1645 543 1102 1.688 1767 1224 .593 1.613 .755 .69
9 533 520 499 564 34 -44 539 465 518 605 40 -99 0 0 327 304 162 286 35 13 21 3 -10 -59 null null null .726 .799 4.705 80 416 97.703 .03 100 3440 15690 21 31 152 162 -100 547 594 -46 null 489 -104 null null null null
10 462 411 478 547 -16 -136 416 368 495 589 -62 -179 0 0 284 217 161 261 25 2 17 1 -152 -241 null null null .923 .885 4.488 80 386 2.522 .18 100 3600 15690 21 31 168 178 -100 433 576 -143 null 387 -188 null null null null
11 808 712 455 513 353 199 512 558 489 573 57 45 0 0 591 479 187 291 43 32 38 23 552 102 1.774 .564 .789 1.153 1.095 3.632 80 386 .774 .6 100 3760 15690 21 31 184 194 -100 749 540 209 .593 587 47 1.685 .831 -.753 -.267
12 677 719 444 472 233 247 589 561 555 558 145 89 0 0 476 525 1674 1018 1 7 0 1 480 234 .943 1.06 .614 .847 .864 2.576 80 418 1.314 .51 100 3920 15690 21 31 200 210 -100 757 497 260 1.116 591 94 .896 .646 .158 -.63
13 2386 1576 372 307 2014 1269 1986 1592 481 360 1614 1285 0 0 1564 745 441 220 75 91 75 83 3283 2899 1.587 .63 .796 .7 .581 2.844 12 104 .619 .4 50 4070 15690 23 28 217 222 0 1659 323 1336 .663 1676 1353 1.508 .838 -.592 -.255
14 1054 1363 465 476 589 887 1058 1378 529 544 593 902 0 0 311 437 262 405 90 90 59 65 1476 1495 .664 1.506 1.521 1.503 1.563 2.029 32 233 1.83 .38 70 4220 15690 22 29 231 238 0 1435 501 934 1.585 1451 949 .631 1.601 .665 .679
15 916 3012 508 572 408 2440 1079 2829 607 816 571 2257 0 0 419 1090 383 861 58 91 16 75 2848 2828 .167 5.98 3.953 4.383 5.437 1.736 12 104 4.86 .54 50 4360 15690 23 28 246 251 0 3171 602 2568 6.295 2978 2376 .159 4.161 2.654 2.057
16 607 611 421 413 186 198 423 401 455 468 2 -12 0 0 499 458 188 253 32 33 27 27 384 -10 .939 1.065 null .888 .914 3.026 80 450 1.126 .53 100 4570 15690 21 31 265 275 -50 643 435 208 1.121 422 -13 .892 null .164 null
17 1429 1543 608 514 821 1029 1601 1631 627 593 993 1117 0 0 569 422 245 328 83 91 83 75 1850 2110 .798 1.253 1.125 1.048 1.101 1.307 12 84 1.005 .56 50 4680 15690 23 28 278 283 -100 1624 541 1083 1.319 1717 1176 .758 1.184 .4 .244
18 860 908 459 490 401 418 933 816 500 542 474 326 0 0 577 586 159 253 65 56 53 43 819 800 .959 1.042 .688 .873 .904 2.653 32 176 1.208 .39 60 4870 15690 23 29 297 303 -100 956 516 440 1.097 859 343 .911 .724 .134 -.466
19 641 683 459 520 182 163 568 626 590 582 109 106 0 0 303 281 1913 291 0 28 0 7 345 215 1.117 .896 .972 .841 .792 3.961 80 448 .039 .08 100 5050 15690 21 31 313 323 -100 719 547 172 .943 659 112 1.061 1.024 -.085 .034
20 1266 934 412 374 854 560 1255 1009 863 427 843 635 0 0 136 421 4081 253 0 75 0 66 1414 1478 1.525 .656 .753 .549 .762 2.98 12 98 .639 .46 50 5180 15690 23 28 328 333 -100 983 394 589 .69 1062 668 1.449 .793 -.535 -.335

Total number of rows: 11520

Table truncated, full table size 2562 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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