NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM211789 Query DataSets for GSM211789
Status Public on Jul 20, 2007
Title sigB KCl 0min vs 05 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 5min
Organism Streptomyces coelicolor
Characteristics sigB KCl 5min
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 = 1550, 15570; 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 = 39.02; Parameter Scan Time = 10:35:29; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71691; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.36; 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 = 39.02; Parameter Scan Time = 10:35:29; Parameter PMT Volts = 780; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71653; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.05; 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/2003-12/47416.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
1 206 256 185 214 21 42 187 244 222 262 2 30 0 0 84 110 377 437 1 2 0 0 63 32 .5 2 15 1.672 1.639 4.003 80 472 6.842 .11 100 1860 15900 28 38 26 36 -50 296 248 49 2.315 282 35 .432 17.362 1.211 4.118
2 249 281 189 228 60 53 191 274 198 233 2 46 0 0 194 105 136 82 15 36 8 12 113 48 1.132 .883 23 1.172 .927 4.917 80 426 .548 .32 100 2030 15900 28 38 43 53 -50 325 264 61 1.022 317 53 .978 26.621 .032 4.735
3 232 264 197 234 35 30 224 266 200 247 27 32 0 0 74 95 50 90 32 23 15 8 65 59 1.167 .857 1.185 1.535 1.341 3.623 80 381 15.85 .05 100 2190 15900 28 38 59 69 -50 306 271 35 .992 308 37 1.008 1.372 -.011 .456
4 1378 1521 208 247 1170 1274 1106 1325 209 259 898 1078 0 0 988 787 50 99 92 98 89 95 2444 1976 .918 1.089 1.2 1.259 1.007 2.534 120 480 .944 .84 120 2350 15900 27 39 74 86 0 1760 286 1475 1.26 1534 1248 .793 1.389 .334 .475
5 670 686 213 237 457 449 568 599 214 253 355 362 0 0 495 461 53 103 77 75 75 67 906 717 1.018 .982 1.02 1.035 .99 3.464 80 431 .965 .71 110 2490 15900 27 38 88 99 0 794 274 520 1.137 693 419 .879 1.18 .185 .239
6 540 356 217 234 323 122 500 323 245 245 283 89 0 0 347 220 109 95 68 43 62 34 445 372 2.648 .378 .314 .548 .482 2.703 32 173 .437 .53 60 2660 15910 31 37 108 114 -100 412 271 141 .437 374 103 2.287 .364 -1.194 -1.458
7 1273 1177 203 248 1070 929 1130 1112 216 259 927 864 0 0 763 662 78 99 95 88 90 83 1999 1791 1.152 .868 .932 .809 .901 3.545 120 489 .849 .82 120 2840 15910 28 40 123 135 0 1362 287 1075 1.005 1287 1000 .995 1.079 .007 .109
8 848 996 194 242 654 754 685 860 199 254 491 618 0 0 507 551 44 116 92 91 90 78 1408 1109 .867 1.153 1.259 1.427 1.233 3.081 80 378 1.184 .81 100 2990 15900 28 38 139 149 0 1153 280 873 1.334 995 715 .749 1.457 .416 .543
9 583 879 195 236 388 643 539 800 199 252 344 564 0 0 321 455 47 108 86 92 77 82 1031 908 .603 1.657 1.64 1.697 1.435 2.829 80 488 2 .6 110 3170 15900 27 38 156 167 0 1017 273 744 1.918 926 653 .521 1.898 .94 .924
10 646 497 213 258 433 239 605 409 230 267 392 151 0 0 338 243 93 112 81 62 78 40 672 543 1.812 .552 .385 .576 .66 3.423 32 170 .654 .56 60 3320 15900 30 36 174 180 0 575 299 277 .639 473 175 1.565 .446 -.646 -1.165
11 1775 1125 207 240 1568 885 1003 741 215 249 796 501 0 0 1750 922 67 96 95 85 90 77 2453 1297 1.772 .564 .629 .542 .546 3.033 80 395 .514 .89 100 3500 15900 28 38 190 200 0 1302 278 1024 .653 858 580 1.531 .728 -.614 -.457
12 1202 1132 205 240 997 892 1087 1094 207 243 882 854 0 0 673 604 50 81 95 90 90 87 1889 1736 1.118 .895 .968 1.001 .859 2.222 80 440 .867 .83 110 3630 15900 27 38 202 213 0 1310 278 1032 1.036 1266 988 .966 1.121 .05 .164
13 2190 1552 212 228 1978 1324 2012 1409 214 238 1800 1181 0 0 1512 995 50 82 96 94 96 88 3302 2981 1.494 .669 .656 .67 .624 2.803 52 318 .636 .86 90 3810 15900 28 37 221 230 0 1796 264 1532 .775 1631 1367 1.291 .759 -.368 -.397
14 1698 1842 198 214 1500 1628 1745 1857 206 229 1547 1643 0 0 673 599 64 85 100 100 98 100 3128 3190 .921 1.085 1.062 1.14 1.051 1.81 80 458 1.037 .9 110 3950 15890 26 37 234 245 0 2132 248 1884 1.256 2149 1902 .796 1.229 .329 .298
15 1328 1738 195 220 1133 1518 984 1460 201 228 789 1240 0 0 960 1166 65 83 96 100 92 98 2651 2029 .746 1.34 1.572 1.478 1.429 2.183 80 483 1.323 .86 110 4120 15890 26 37 251 262 0 2012 255 1757 1.551 1690 1435 .645 1.819 .633 .863
16 1253 2628 202 220 1051 2408 960 2225 209 224 758 2005 0 0 919 1683 58 79 91 97 90 95 3459 2763 .436 2.291 2.645 2.259 2.398 2.707 80 462 2.364 .81 110 4290 15890 26 37 268 279 0 3042 255 2787 2.652 2575 2321 .377 3.062 1.407 1.614
17 1805 1619 189 209 1616 1410 1506 1312 190 216 1317 1103 0 0 1074 1051 57 78 99 99 97 97 3026 2420 1.146 .873 .838 .848 .82 2.399 120 527 .907 .88 130 4460 15890 25 38 284 297 0 1874 242 1632 1.01 1519 1277 .99 .969 .014 -.045
18 1577 1673 173 202 1404 1471 1404 1578 176 209 1231 1376 0 0 819 888 45 78 100 95 96 95 2875 2607 .954 1.048 1.118 .996 1.037 2.916 120 386 1.079 .86 120 4600 15900 27 39 299 311 0 1936 234 1703 1.213 1826 1593 .825 1.294 .278 .372
19 1068 1412 175 204 893 1208 1026 1418 186 209 851 1214 0 0 536 695 80 75 96 96 93 94 2101 2065 .739 1.353 1.427 1.331 1.285 2.255 120 442 1.421 .82 120 4750 15890 26 38 314 326 0 1634 236 1398 1.566 1641 1405 .639 1.651 .647 .723
20 954 830 193 205 761 625 935 794 193 214 742 589 0 0 552 506 45 79 88 83 85 77 1386 1331 1.218 .821 .794 .723 .741 2.773 120 480 .843 .78 120 4920 15890 26 38 331 343 0 961 237 723 .951 919 682 1.052 .919 -.073 -.122

Total number of rows: 11520

Table truncated, full table size 2560 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap