NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM89757 Query DataSets for GSM89757
Status Public on Dec 29, 2005
Title J45 CD45 negative 0 hours, #2
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name J45 CD45 negative 0 hours
Organism Homo sapiens
Characteristics J45 CD45 negative 0 hours
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stimulation, Jurkat cells
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16227.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 Dec 28, 2005
Last update date Sep 28, 2006
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 GPL3084
Series (1)
GSE3922 T cell Basal Signaling

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 1444 951 414 259 1030 692 1405 943 421 271 991 684 0 0 331 274 119 114 100 100 100 98 1722 1675 1.488 .672 .69 .649 .662 1.633 80 440 .641 .8 110 2150 8900 26 37 46 57 0 842 229 612 .595 835 605 1.682 .611 -.75 -.711 -.711
2 3380 6082 417 256 2963 5826 3346 5639 424 269 2929 5383 0 0 1019 2526 125 110 100 100 100 100 8789 8312 .509 1.966 1.838 1.922 1.954 1.398 80 340 2.117 .92 110 2280 8890 25 36 59 70 0 5382 227 5156 1.74 4990 4764 .575 1.626 .799 .702 .702
3 4743 10088 420 247 4323 9841 4849 10507 432 269 4429 10260 0 0 1505 3316 123 124 100 100 100 100 14164 14689 .439 2.276 2.317 2.34 2.2 1.48 80 346 2.314 .95 110 2420 8890 25 36 73 84 0 8927 219 8709 2.015 9298 9080 .496 2.05 1.01 1.036 1.036
4 1474 1174 433 238 1041 936 1467 1174 438 263 1034 936 0 0 350 319 118 127 98 98 98 97 1977 1970 1.112 .899 .905 .886 .901 1.491 80 319 .837 .86 110 2560 8890 25 36 87 98 0 1039 211 828 .796 1039 828 1.257 .801 -.33 -.32 -.32
5 1731 1396 393 239 1338 1157 1723 1392 418 254 1330 1153 0 0 429 380 123 111 97 100 97 100 2495 2483 1.156 .865 .867 .827 .795 1.454 80 330 .841 .87 110 2690 8890 25 36 100 111 0 1235 212 1024 .765 1232 1020 1.307 .767 -.386 -.382 -.382
6 1745 1162 403 241 1342 921 1734 1194 417 255 1331 953 0 0 303 356 118 112 100 98 100 98 2263 2284 1.457 .686 .716 .659 .71 1.543 80 363 .674 .84 110 2830 8890 25 36 114 125 0 1028 213 815 .607 1057 843 1.647 .634 -.719 -.658 -.658
7 2595 2240 406 246 2189 1994 2633 2356 411 258 2227 2110 0 0 736 719 114 118 98 100 98 100 4183 4337 1.098 .911 .947 .896 .896 1.501 80 383 .907 .92 110 2960 8880 24 35 127 138 0 1982 218 1765 .806 2085 1867 1.241 .838 -.311 -.254 -.254
8 1973 1908 400 259 1573 1649 2003 1909 412 270 1603 1650 0 0 455 564 121 130 100 100 100 100 3222 3253 .954 1.048 1.029 1.038 1.02 1.442 80 494 1.05 .91 110 3100 8880 24 35 141 152 0 1688 229 1459 .928 1689 1460 1.078 .911 -.108 -.135 -.135
9 1115 612 396 253 719 359 1165 577 415 272 769 324 0 0 297 217 128 134 98 86 91 65 1078 1093 2.003 .499 .421 .477 .481 2.221 80 437 .472 .68 100 3400 8880 25 35 172 182 0 542 224 318 .442 511 287 2.263 .373 -1.178 -1.423 -1.423
10 2890 4834 394 240 2496 4594 2953 4712 408 253 2559 4472 0 0 859 1942 113 108 100 100 98 100 7090 7031 .543 1.841 1.748 1.801 1.739 1.486 80 404 1.936 .93 110 3560 8890 25 36 187 198 0 4278 212 4065 1.629 4170 3958 .614 1.547 .704 .629 .629
11 3992 9349 403 231 3589 9118 4077 9468 406 246 3674 9237 0 0 1305 3044 114 113 100 100 100 100 12707 12911 .394 2.541 2.514 2.577 2.492 1.37 80 380 2.582 .95 100 3710 8880 25 35 203 213 0 8273 204 8069 2.248 8379 8174 .445 2.225 1.169 1.154 1.154
12 1355 954 384 232 971 722 1332 900 391 248 948 668 0 0 286 352 110 111 100 96 98 96 1693 1616 1.345 .744 .705 .703 .715 1.707 80 448 .764 .81 110 3870 8870 23 34 218 229 0 844 205 639 .658 796 591 1.52 .624 -.604 -.681 -.681
13 1604 1420 381 244 1223 1176 1637 1381 387 262 1256 1137 0 0 379 533 107 109 100 100 100 100 2399 2393 1.04 .962 .905 .921 .869 1.643 80 433 .965 .82 110 4030 8870 23 34 234 245 0 1257 216 1041 .851 1222 1006 1.175 .801 -.233 -.32 -.32
14 1547 1031 376 241 1171 790 1543 1035 390 256 1167 794 0 0 351 348 115 107 100 100 100 96 1961 1961 1.482 .675 .68 .625 .636 1.682 80 351 .657 .82 100 4180 8870 24 34 250 260 0 912 213 699 .597 916 703 1.675 .602 -.744 -.732 -.732
15 1704 1641 378 236 1326 1405 1705 1625 391 249 1327 1389 0 0 494 520 115 110 100 100 98 100 2731 2716 .944 1.06 1.047 1.081 1.08 1.456 80 379 1.063 .91 100 4330 8880 25 35 265 275 0 1452 209 1243 .938 1438 1229 1.066 .926 -.093 -.11 -.11
16 1401 1132 387 229 1014 903 1438 1149 400 250 1051 920 0 0 332 339 118 107 100 100 100 98 1917 1971 1.123 .891 .875 .869 .887 1.638 80 429 .864 .84 110 4490 8880 24 35 280 291 0 1002 203 799 .788 1017 814 1.269 .775 -.344 -.368 -.368
17 1881 1030 384 233 1497 797 1838 1000 392 250 1454 767 0 0 577 356 117 107 100 100 98 95 2294 2221 1.878 .532 .528 .518 .516 1.742 80 408 .495 .83 110 4650 8880 24 35 296 307 0 912 206 705 .471 885 679 2.122 .467 -1.086 -1.099 -1.099
18 2167 2866 377 239 1790 2627 2035 2688 398 265 1658 2449 0 0 518 782 184 261 100 100 100 100 4417 4107 .681 1.468 1.477 1.466 1.491 1.388 80 421 1.484 .9 110 4800 8880 24 35 311 322 0 2536 212 2325 1.299 2379 2167 .77 1.307 .377 .386 .386
19 2813 3903 390 247 2423 3656 2797 3861 404 278 2407 3614 0 0 864 1108 180 262 100 100 98 100 6079 6021 .663 1.509 1.501 1.547 1.532 1.43 80 431 1.487 .94 110 4960 8880 24 35 327 338 0 3454 219 3235 1.335 3417 3198 .749 1.329 .417 .41 .41
20 3192 5057 391 248 2801 4809 3213 4754 401 264 2822 4506 0 0 1022 1519 114 114 98 100 98 100 7610 7328 .582 1.717 1.597 1.754 1.711 1.372 80 379 1.701 .94 110 5120 8890 25 36 343 354 0 4475 219 4256 1.519 4207 3988 .658 1.413 .603 .499 .499

Total number of rows: 37632

Table truncated, full table size 8801 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap