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Sample GSM211783 Query DataSets for GSM211783
Status Public on Jul 20, 2007
Title J1501 KCl 0min vs 30min
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 30min
Organism Streptomyces coelicolor
Characteristics J1501 KCl 30min
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 = 1930, 15520; 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 = 38.20; Parameter Scan Time = 09:32:12; Parameter PMT Volts = 750; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68407; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.22; 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 = 38.20; Parameter Scan Time = 09:32:12; Parameter PMT Volts = 780; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68369; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.99; 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/2003-11/46305.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 1252 1657 981 1073 271 584 1253 1691 1041 1203 272 618 0 0 325 641 393 524 33 58 0 16 855 890 .464 2.155 2.272 1.901 1.42 3.3 12 90 7.579 .27 50 2300 15690 14 19 34 39 -100 1419 919 500 1.846 1449 529 .542 1.946 .884 .961
2 5130 4181 1001 1068 4129 3113 1264 1367 1062 1136 263 299 3 0 13519 8353 304 300 40 50 28 28 7242 562 1.326 .754 1.137 1.155 1.251 3.107 32 102 .22 .46 60 2470 15770 22 28 51 57 -100 3582 915 2667 .646 1171 256 1.548 .974 -.631 -.038
3 987 1088 950 1076 37 12 968 1022 1057 1119 18 -54 0 0 289 366 1034 323 1 15 0 5 49 -36 3.083 .324 null 1.795 1.625 4.03 80 421 .264 .33 100 2570 15700 13 23 59 69 -50 932 922 10 .278 875 -46 3.599 null -1.848 null
4 1123 1283 949 1101 174 182 719 461 1002 1117 -230 -640 0 0 945 1442 484 250 26 30 19 28 356 -870 .956 1.046 null 1.993 1.899 2.173 52 286 1.519 .36 80 2740 15690 13 21 77 85 0 1099 943 156 .896 395 -548 1.116 null -.158 null
5 665 452 903 1044 -238 -592 566 322 942 1069 -337 -722 0 0 334 311 315 230 7 1 2 0 -830 -1059 null null null 1.868 1.884 2.849 80 401 1.946 .51 100 2900 15710 14 24 92 102 -50 387 894 -507 null 276 -618 null null null null
6 1255 789 919 1073 336 -284 936 825 994 1103 17 -248 0 0 1158 469 482 345 23 5 12 1 52 -231 null null null 1.824 2.175 4.569 80 405 .041 .11 100 3060 15710 14 24 108 118 -50 676 919 -243 null 707 -212 null null null null
7 2149 2338 985 1108 1164 1230 2365 2865 1050 1196 1380 1757 0 0 900 1403 444 545 78 59 65 59 2394 3137 .946 1.057 1.273 1.528 1.488 3.771 32 176 1.563 .48 60 3230 15710 16 22 127 133 0 2003 949 1054 .905 2454 1505 1.105 1.091 -.144 .125
8 2406 1007 925 1035 1481 -28 2040 1186 1277 1059 1115 151 0 0 1837 473 2151 261 3 31 3 9 1453 1266 null null .135 .221 .202 1.952 32 176 113.817 .03 60 3390 15710 16 22 143 149 -100 863 887 -24 null 1016 129 null .116 null -3.108
9 1266 1155 927 1058 339 97 1177 1211 1164 1129 250 153 0 0 509 562 1736 706 1 16 0 0 436 403 3.495 .286 .612 1.188 1.281 2.634 80 416 .056 .09 100 3550 15710 14 24 157 167 -50 989 906 83 .245 1037 131 4.08 .524 -2.028 -.932
10 1255 847 929 1089 326 -242 1196 870 1007 1162 267 -219 0 0 536 359 1118 724 11 1 0 0 84 48 null null null .661 .729 5.757 80 386 .114 .12 100 3710 15710 14 24 173 183 -50 726 933 -207 null 745 -188 null null null null
11 1210 1157 935 1077 275 80 755 679 1457 1104 -180 -398 0 0 974 1131 4253 355 1 27 0 21 355 -578 3.438 .291 null 1.597 1.749 2.768 80 386 .874 .41 100 3870 15710 14 24 189 199 -50 991 923 69 .249 582 -341 4.013 null -2.005 null
12 1246 1246 968 1045 278 201 947 1018 1749 1102 -21 -27 0 0 708 787 4473 429 0 36 0 23 479 -48 1.383 .723 null 1.325 1.275 2.84 80 426 .006 .05 100 4030 15710 14 24 205 215 -50 1067 895 172 .619 872 -23 1.615 null -.691 null
13 4470 4269 865 873 3605 3396 4477 3784 1473 998 3612 2911 0 0 2249 1371 2497 708 75 100 25 100 7001 6523 1.062 .942 .806 1.369 .974 4.537 12 104 .263 .33 50 4190 15710 16 21 223 228 -100 3657 748 2909 .807 3242 2494 1.239 .69 -.309 -.535
14 1689 981 941 1036 748 -55 1033 883 1325 1132 92 -153 0 0 3194 645 2401 1197 5 2 3 0 693 -61 null null null 1.167 1.294 2.582 80 434 161.881 .04 100 4360 15710 14 24 238 248 -50 840 887 -47 null 756 -131 null null null null
15 1792 1414 953 1059 839 355 1288 1275 1121 1094 335 216 0 0 1629 807 963 311 36 46 15 35 1194 551 2.363 .423 .645 .964 .871 4.046 80 434 .113 .23 100 4520 15710 14 24 254 264 -50 1211 907 304 .362 1092 185 2.759 .552 -1.464 -.856
16 3039 1693 973 918 2066 775 2398 1767 1197 979 1425 849 0 0 1837 427 921 411 66 75 41 50 2841 2274 2.666 .375 .596 .553 .456 2.679 12 104 .279 .34 50 4700 15710 16 21 274 279 -100 1450 786 664 .321 1514 727 3.112 .51 -1.638 -.97
17 2131 1847 944 1043 1187 804 2209 1766 1328 1118 1265 723 0 0 1389 1174 3288 396 1 51 1 48 1991 1988 1.476 .677 .572 1.045 .988 2.682 52 291 .483 .35 80 4860 15720 16 24 289 297 -100 1582 893 689 .58 1513 619 1.723 .49 -.785 -1.03
18 1889 2284 867 978 1022 1306 2174 2345 1215 1004 1307 1367 0 0 762 536 1585 426 33 91 0 83 2328 2674 .783 1.278 1.046 1.285 1.081 2.175 12 104 -1 -1 50 4990 15710 16 21 303 308 -100 1957 838 1119 1.095 2009 1171 .914 .896 .131 -.158
19 1573 2908 937 981 636 1927 1789 2756 1127 1083 852 1775 0 0 639 405 1156 616 25 100 0 100 2563 2627 .33 3.03 2.083 2.501 2.194 1.749 12 104 1.415 .11 50 5150 15710 16 21 319 324 -100 2491 840 1651 2.595 2361 1521 .385 1.785 1.376 .836
20 1439 1110 933 1049 506 61 968 993 993 1091 35 -56 0 0 1228 663 396 399 37 35 33 16 567 -21 8.295 .121 null 1.224 1.31 3.227 80 447 .17 .23 100 5330 15710 14 24 335 345 -50 951 899 52 .103 851 -48 9.683 null -3.276 null

Total number of rows: 11520

Table truncated, full table size 2644 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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