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Sample GSM173058 Query DataSets for GSM173058
Status Public on Sep 28, 2007
Title Coronary SM Serum St, 3 hr
Sample type RNA
 
Channel 1
Source name Strategene
Organism Homo sapiens
Characteristics Strategene
LabeledExtract: 45339.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Coronary SM Serum St, 3hr
Organism Homo sapiens
Characteristics Coronary SM Serum St, 3hr
LabeledExtract: 45339.Channel_2
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi
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 = 38.39; Parameter Scan Time = 10:49:16; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125655; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi
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 = 38.39; Parameter Scan Time = 10:49:16; Parameter PMT Volts = 620; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490756; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.90; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi
Description Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45339.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 Mar 05, 2007
Last update date Sep 28, 2007
Contact name Jen-Tsan Ashley Chi
E-mail(s) jentsan.chi@duke.edu
Phone 919-668-4759
Fax 919-668-4777
Organization name Duke University
Department Duke Institute for Genome Sciences & Policy
Lab CIEMAS 2177A
Street address 101 Science Drive
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL3526
Series (1)
GSE7195 Smooth Muscle Cells

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
1 305 387 105 186 200 201 321 400 128 206 216 214 0 0 119 182 138 86 71 73 30 59 401 430 .995 1.005 .991 1.198 1.056 2.271 52 343 1.608 .347 90 1230 6070 102 111 66 75 0 672 323 349 1.746 695 372 .573 1.721 .804 .783
2 6047 1304 129 248 5918 1056 5555 1102 216 259 5426 854 0 0 3407 697 275 97 96 90 96 90 6974 6280 5.604 .178 .157 .167 .192 1.764 32 192 .163 .753 70 1370 6070 103 110 81 88 0 2265 431 1835 .31 1914 1484 3.226 .273 -1.69 -1.871
3 3008 1143 111 213 2897 930 2552 1086 139 223 2441 873 0 0 2136 680 144 88 95 88 90 85 3827 3314 3.115 .321 .358 .328 .352 1.96 120 557 .293 .812 120 1510 6070 101 113 93 105 0 1986 370 1616 .558 1887 1517 1.793 .621 -.842 -.687
4 1374 512 127 257 1247 255 1210 579 137 258 1083 322 0 0 698 270 49 98 100 66 100 66 1502 1405 4.89 .204 .297 .264 .233 1.372 12 104 .236 .565 50 1660 6070 104 109 111 116 0 889 446 443 .355 1006 559 2.815 .517 -1.493 -.953
5 1365 3846 115 226 1250 3620 1382 3776 131 278 1267 3550 0 0 726 1996 70 212 94 100 90 96 4870 4817 .345 2.896 2.802 3.187 3.137 1.89 52 381 3.206 .798 90 1810 6060 101 110 124 133 0 6682 393 6289 5.031 6560 6167 .199 4.868 2.331 2.283
6 306 547 112 218 194 329 222 384 116 234 110 166 0 0 201 374 28 93 69 61 57 48 523 276 .59 1.696 1.509 1.784 1.756 3.402 52 243 2.119 .649 80 1970 6060 102 110 141 149 -50 950 379 572 2.946 667 288 .339 2.622 1.559 1.391
7 2328 1261 112 227 2216 1034 2264 1378 123 246 2152 1151 0 0 1240 545 73 100 100 96 100 92 3250 3303 2.143 .467 .535 .455 .465 1.675 52 249 .408 .829 80 2090 6080 104 112 153 161 0 2191 394 1796 .811 2394 2000 1.234 .929 -.303 -.106
8 1224 730 122 288 1102 442 1454 751 149 291 1332 463 0 0 699 364 107 113 81 84 78 75 1544 1795 2.493 .401 .348 .645 .428 3.86 32 166 .414 .596 60 2270 6070 104 110 172 178 0 1268 500 768 .697 1305 804 1.435 .604 -.521 -.728
9 582 642 124 298 458 344 606 710 139 307 482 412 0 0 277 309 54 108 87 75 84 65 802 894 1.331 .751 .855 .968 .944 2.762 32 161 1.078 .541 60 2400 6070 104 110 185 191 0 1115 518 598 1.305 1233 716 .766 1.485 .384 .57
10 707 463 113 251 594 212 725 461 134 289 612 210 0 0 355 191 102 249 88 44 82 7 806 822 2.802 .357 .343 .42 .414 2.512 52 266 .372 .34 80 2550 6060 102 110 199 207 0 804 436 368 .62 801 365 1.613 .596 -.69 -.746
11 768 7440 107 208 661 7232 281 1562 124 244 174 1354 0 0 946 9705 75 209 65 89 51 80 7893 1528 .091 10.941 7.782 9.321 9.868 2.751 120 429 11.705 .789 120 2710 6080 102 114 213 225 0 12925 361 12564 19.008 2714 2352 .053 13.519 4.249 3.757
12 6195 5945 107 208 6088 5737 2077 2035 125 234 1970 1827 0 0 8436 7322 80 127 90 93 80 85 11825 3797 1.061 .942 .927 1.153 .969 2.802 120 434 .878 .872 120 2840 6080 102 114 226 238 0 10328 361 9967 1.637 3535 3174 .611 1.611 .711 .688
13 867 2591 110 225 757 2366 432 1503 117 249 322 1278 0 0 851 2539 37 120 77 83 72 80 3123 1600 .32 3.125 3.969 3.225 3.103 2.497 80 334 3.161 .891 100 2990 6070 102 112 242 252 0 4501 391 4110 5.43 2611 2220 .184 6.895 2.441 2.786
14 311 490 112 255 199 235 352 522 118 286 240 267 0 0 158 273 35 125 75 65 69 51 434 507 .847 1.181 1.113 1.37 1.432 2.927 52 247 2.229 .381 80 3140 6060 102 110 258 266 -50 851 443 408 2.052 907 464 .487 1.933 1.037 .951
15 400 396 112 244 288 152 480 434 182 358 368 190 0 0 283 274 373 457 48 15 0 0 440 558 1.895 .528 .516 1.36 1.116 3.156 52 231 1.49 .531 80 3290 6080 104 112 273 281 0 688 424 264 .917 754 330 1.091 .897 -.125 -.157
16 5778 6961 108 241 5670 6720 2886 4725 152 317 2778 4484 0 0 5456 6232 297 368 92 95 82 86 12390 7262 .844 1.185 1.614 1.368 1.266 2.177 80 371 1.164 .908 110 3430 6080 102 113 285 296 0 12093 419 11675 2.059 8209 7790 .486 2.804 1.042 1.488
17 2657 4819 124 323 2533 4496 2753 5029 252 507 2629 4706 0 0 1734 3355 470 810 93 84 75 68 7029 7335 .563 1.775 1.79 1.641 1.761 1.624 32 147 1.905 .886 60 3560 6060 103 109 301 307 0 8372 561 7811 3.084 8737 8176 .324 3.11 1.625 1.637
18 1221 600 158 353 1063 247 1210 591 258 351 1052 238 0 0 318 231 308 156 100 58 100 41 1310 1290 4.304 .232 .226 .256 .305 2.052 12 104 .22 .235 50 3700 6060 103 108 315 320 0 1042 613 429 .404 1027 413 2.477 .393 -1.309 -1.347
19 2391 1458 112 228 2279 1230 880 690 184 272 768 462 0 0 3133 1698 247 170 67 72 60 58 3509 1230 1.853 .54 .602 .729 .669 3.414 120 506 .499 .754 120 3890 6070 101 113 331 343 0 2533 396 2137 .938 1199 803 1.067 1.045 -.093 .064
20 2202 1711 112 242 2090 1469 1536 947 134 290 1424 705 0 0 2128 1535 118 162 85 78 75 65 3559 2129 1.423 .703 .495 .691 .8 3.356 80 346 .681 .827 110 4030 6070 101 112 345 356 0 2972 420 2552 1.221 1645 1225 .819 .86 .288 -.217

Total number of rows: 41472

Table truncated, full table size 9167 Kbytes.




Supplementary data files not provided
Processed data not provided for this record
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