NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM67497 Query DataSets for GSM67497
Status Public on Aug 05, 2005
Title HSF1 +/+ Mouse Fibroblasts Heat Shock 4 hours Scanner7
Sample type RNA
 
Channel 1
Source name Pooled mRNA from heat shocked (1 hr) and non-heat-shocked mouse fibroblasts
Organism Mus musculus
Characteristics Pooled mRNA from heat shocked (1 hr) and non-heat-shocked mouse fibroblasts
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name HSF1 +/+ Mouse Fibroblasts Heat Shock 4 hours mRNA
Organism Mus musculus
Characteristics HSF1 +/+ Mouse Fibroblasts Heat Shock 4 hours mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37431.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 Aug 05, 2005
Last update date Sep 22, 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 GPL2727
Series (1)
GSE3074 HSF1 Mouse Fibroblast Heat Shock - Scanner7

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 2123 1456 726 381 1397 1075 2222 1461 726 383 1496 1080 0 0 783 564 117 101 92 92 92 92 2472 2576 1.3 .77 .722 .726 .779 1.774 80 412 .747 .93 100 2310 7890 54 64 73 83 0 1252 328 924 .662 1256 929 1.511 .621 -.596 -.688
2 2755 3206 755 396 2000 2810 2772 3228 759 408 2017 2832 0 0 1032 1492 120 116 94 98 94 98 4810 4849 .712 1.405 1.404 1.332 1.359 1.315 52 289 1.434 .95 90 2450 7880 53 62 87 96 0 2757 340 2416 1.208 2775 2435 .828 1.207 .273 .272
3 3460 5577 799 422 2661 5155 3362 5547 810 434 2563 5125 0 0 1257 2332 127 113 97 100 97 100 7816 7688 .516 1.937 2 1.936 1.845 1.279 80 396 1.95 .97 100 2600 7890 54 64 102 112 0 4795 363 4432 1.666 4769 4406 .6 1.719 .736 .782
4 2007 1150 825 424 1182 726 2001 1113 847 446 1176 689 0 0 611 400 162 124 92 94 90 92 1908 1865 1.628 .614 .586 .645 .616 1.748 52 315 .568 .88 90 2750 7880 53 62 117 126 0 989 365 624 .528 957 592 1.894 .504 -.921 -.989
5 2496 1584 878 445 1618 1139 2686 1647 922 485 1808 1202 0 0 620 526 299 206 96 96 92 92 2757 3010 1.421 .704 .665 .665 .704 1.628 52 305 .694 .91 90 2890 7870 52 61 131 140 0 1362 383 979 .605 1416 1033 1.652 .572 -.724 -.807
6 4072 8227 855 448 3217 7779 4176 8681 889 471 3321 8233 0 0 1421 2947 257 154 93 100 92 100 10996 11554 .414 2.418 2.479 2.588 2.426 1.492 80 438 2.394 .96 110 3040 7890 53 64 145 156 0 7074 385 6688 2.079 7464 7079 .481 2.132 1.056 1.092
7 2297 1677 930 491 1367 1186 2296 1639 946 503 1366 1148 0 0 707 629 206 129 92 94 92 92 2553 2514 1.153 .868 .84 .786 .835 1.571 52 248 .865 .92 80 3180 7880 54 62 161 169 0 1442 422 1020 .746 1409 987 1.341 .723 -.423 -.469
8 2644 1781 928 522 1716 1259 2722 1760 937 524 1794 1238 0 0 530 496 179 132 100 100 100 100 2975 3032 1.363 .734 .69 .713 .651 1.301 32 151 .74 .92 60 3320 7870 54 60 176 182 0 1531 449 1082 .631 1513 1064 1.585 .593 -.665 -.753
9 4618 7818 907 482 3711 7336 4494 7806 920 491 3587 7324 0 0 1553 2987 183 122 100 100 98 100 11047 10911 .506 1.977 2.042 2.021 1.899 1.403 80 393 2 .97 100 3470 7890 54 64 189 199 0 6722 414 6308 1.7 6712 6297 .588 1.756 .765 .812
10 1080 633 859 483 221 150 977 627 1312 956 118 144 0 0 449 216 4487 4474 0 0 0 0 371 262 1.473 .679 1.22 .576 .574 2.905 52 246 .642 .71 80 3620 7880 54 62 205 213 0 544 415 129 .584 539 124 1.714 1.049 -.777 .069
11 2612 2819 918 510 1694 2309 2821 3078 1280 897 1903 2568 0 0 833 902 3982 3973 0 0 0 0 4003 4471 .734 1.363 1.349 1.424 1.296 1.557 52 312 1.021 .99 90 3760 7880 53 62 218 227 0 2424 438 1985 1.172 2646 2208 .853 1.16 .229 .214
12 3259 4445 1087 638 2172 3807 3437 4678 1124 664 2350 4040 0 0 1061 1544 247 195 92 100 92 100 5979 6390 .571 1.753 1.719 1.771 1.695 1.294 52 316 1.732 .95 90 3910 7880 53 62 233 242 0 3822 549 3273 1.507 4022 3474 .664 1.478 .592 .564
13 2237 1548 1001 562 1236 986 2157 1528 1043 591 1156 966 0 0 519 494 226 185 96 100 96 93 2222 2122 1.254 .798 .836 .791 .801 1.541 32 215 .807 .9 70 4050 7880 54 61 248 255 0 1331 483 848 .686 1314 831 1.458 .718 -.544 -.477
14 2162 1315 936 504 1226 811 2184 1376 960 516 1248 872 0 0 604 438 215 155 92 90 88 84 2037 2120 1.512 .662 .699 .606 .64 1.526 52 254 .659 .89 80 4200 7890 55 63 263 271 0 1131 433 697 .569 1183 750 1.758 .601 -.814 -.735
15 4465 19625 927 485 3538 19140 4799 21630 945 502 3872 21145 0 0 1501 6734 212 137 100 100 97 100 22678 25017 .185 5.41 5.461 5.719 5.369 1.375 80 351 5.364 .97 100 4350 7890 54 64 277 287 0 16874 417 16457 4.651 18598 18180 .215 4.695 2.218 2.231
16 2201 1555 863 473 1338 1082 2402 1561 890 485 1539 1088 0 0 615 473 189 123 92 98 90 96 2420 2627 1.237 .809 .707 .768 .767 1.587 52 246 .757 .9 80 4500 7880 54 62 293 301 0 1337 407 930 .695 1342 935 1.438 .608 -.524 -.718
17 1249 622 972 538 277 84 1093 628 997 549 121 90 0 0 646 200 177 134 36 34 21 11 361 211 3.298 .303 .744 .561 .459 3.094 52 250 .246 .5 80 4640 7880 54 62 307 315 0 535 463 72 .261 540 77 3.835 .64 -1.939 -.645
18 2941 4593 906 493 2035 4100 2360 3285 934 503 1454 2792 0 0 1830 3295 237 123 81 96 78 96 6135 4246 .496 2.015 1.92 2.081 1.925 1.697 32 161 1.914 .96 60 4780 7900 57 63 322 328 0 3949 424 3525 1.732 2824 2401 .577 1.651 .793 .723
19 1294 628 999 546 295 82 1078 584 1028 566 79 38 0 0 608 257 294 152 32 30 26 19 377 117 3.598 .278 .481 .648 .453 4.329 52 268 .209 .49 80 4930 7880 54 62 336 344 0 540 469 71 .239 502 33 4.184 .414 -2.065 -1.274
20 2154 1619 1150 732 1004 887 2086 1494 1148 737 936 762 0 0 787 685 158 167 88 86 86 80 1891 1698 1.132 .883 .814 .821 .849 1.608 52 246 .84 .89 80 5080 7880 54 62 351 359 0 1392 629 763 .76 1285 655 1.316 .7 -.397 -.515

Total number of rows: 42624

Table truncated, full table size 9743 Kbytes.




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