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Sample GSM67501 Query DataSets for GSM67501
Status Public on Aug 05, 2005
Title HSF1 +/+ Mouse Fibroblasts Heat Shock 2 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 2 hours mRNA
Organism Mus musculus
Characteristics HSF1 +/+ Mouse Fibroblasts Heat Shock 2 hours mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37433.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 2374 1426 920 532 1454 894 2422 1412 931 537 1502 880 0 0 401 282 130 110 100 100 100 97 2348 2382 1.626 .615 .586 .606 .616 1.317 80 385 .597 .93 100 2310 7940 59 69 73 83 0 1355 506 850 .584 1342 836 1.711 .557 -.775 -.845
2 3377 3976 907 540 2470 3436 3467 4086 917 546 2560 3546 0 0 893 1170 121 110 100 100 100 100 5906 6106 .719 1.391 1.385 1.418 1.399 1.287 52 264 1.389 .97 90 2450 7930 58 67 87 96 0 3778 513 3265 1.322 3883 3370 .756 1.316 .403 .397
3 3808 5126 888 535 2920 4591 3794 5251 897 541 2906 4716 0 0 876 1338 130 116 100 100 100 100 7511 7622 .636 1.572 1.623 1.582 1.544 1.214 80 365 1.58 .98 100 2600 7930 58 68 102 112 0 4871 508 4363 1.494 4990 4482 .669 1.542 .579 .625
4 2020 1055 890 523 1130 532 2037 1064 892 538 1147 541 0 0 427 244 130 117 98 96 96 86 1662 1688 2.124 .471 .472 .451 .459 1.462 52 266 .471 .86 90 2750 7940 59 68 117 126 0 1003 497 506 .447 1011 514 2.235 .448 -1.16 -1.158
5 2113 1115 897 539 1216 576 2180 1081 901 548 1283 542 0 0 377 273 124 108 98 95 98 91 1792 1825 2.111 .474 .422 .437 .483 1.764 80 346 .464 .82 100 2890 7930 58 68 131 141 0 1060 512 547 .45 1027 515 2.221 .401 -1.152 -1.317
6 4827 10677 935 562 3892 10115 5040 10836 956 571 4105 10274 0 0 1278 3301 221 155 98 100 98 100 14007 14379 .385 2.599 2.503 2.649 2.575 1.255 80 413 2.616 .98 110 3040 7930 57 68 145 156 0 10147 534 9612 2.47 10298 9764 .405 2.378 1.304 1.25
7 2342 1640 962 579 1380 1061 2384 1644 976 604 1422 1065 0 0 347 316 178 291 100 100 100 92 2441 2487 1.301 .769 .749 .757 .78 1.357 52 313 .872 .86 90 3190 7930 58 67 161 170 0 1559 550 1008 .731 1562 1012 1.369 .712 -.453 -.491
8 2201 1481 953 555 1248 926 2245 1488 960 559 1292 933 0 0 396 312 136 114 100 100 100 100 2174 2225 1.348 .742 .722 .734 .784 1.42 52 290 .715 .88 90 3330 7920 57 66 175 184 0 1407 527 880 .705 1414 887 1.418 .686 -.504 -.543
9 4727 7606 953 566 3774 7040 4563 7104 962 567 3610 6538 0 0 1877 3363 141 111 100 100 98 100 10814 10148 .536 1.865 1.811 1.932 1.892 1.255 80 337 1.855 .98 100 3480 7930 58 68 190 200 0 7228 538 6690 1.773 6751 6213 .564 1.721 .826 .783
10 1597 938 964 580 633 358 1352 842 970 587 388 262 0 0 709 383 154 105 71 69 55 61 991 650 1.768 .566 .675 .708 .736 2.291 52 286 .506 .78 90 3610 7920 57 66 203 212 0 891 551 340 .537 800 249 1.861 .642 -.896 -.64
11 2684 3093 968 581 1716 2512 2885 3149 969 583 1917 2568 0 0 831 1172 136 112 96 100 96 96 4228 4485 .683 1.464 1.34 1.449 1.459 1.302 52 322 1.472 .96 90 3760 7920 57 66 218 227 0 2939 552 2387 1.391 2993 2440 .719 1.273 .476 .348
12 2669 2789 951 566 1718 2223 2623 2497 974 569 1672 1931 0 0 1093 1296 248 134 93 97 91 96 3941 3603 .773 1.294 1.155 1.287 1.291 1.502 80 384 1.272 .95 100 3910 7920 57 67 233 243 0 2650 538 2113 1.23 2373 1835 .813 1.098 .298 .134
13 2226 1306 986 595 1240 711 2254 1270 1008 596 1268 675 0 0 466 362 198 122 96 98 94 92 1951 1943 1.744 .573 .532 .546 .556 1.65 52 244 .563 .86 80 4060 7930 59 67 249 257 0 1241 565 676 .545 1207 641 1.835 .506 -.876 -.983
14 2045 1122 962 592 1083 530 2040 1123 988 594 1078 531 0 0 348 188 197 125 100 100 100 90 1613 1609 2.043 .489 .493 .48 .483 1.487 52 288 .48 .83 90 4200 7930 58 67 262 271 0 1066 563 504 .465 1067 505 2.15 .468 -1.104 -1.095
15 4577 19295 957 560 3620 18735 4680 20352 969 563 3723 19792 0 0 1136 5240 153 111 100 100 100 100 22355 23515 .193 5.175 5.316 5.261 5.153 1.181 80 381 5.217 .98 100 4350 7930 58 68 277 287 0 18336 532 17804 4.918 19341 18809 .203 5.052 2.298 2.337
16 2118 1326 948 544 1170 782 2163 1338 963 553 1215 794 0 0 509 306 171 108 96 98 96 94 1952 2009 1.496 .668 .653 .669 .686 1.464 52 301 .61 .88 90 4490 7920 57 66 291 300 0 1260 517 743 .635 1272 755 1.574 .621 -.655 -.687
17 1625 661 952 566 673 95 1551 645 968 574 599 79 0 0 532 148 139 109 84 40 68 21 768 678 7.084 .141 .132 .262 .227 2.55 32 170 .13 .27 60 4640 7930 60 66 308 314 0 628 538 90 .134 613 75 7.455 .125 -2.898 -2.996
18 3140 4875 992 574 2148 4301 2695 3568 1000 584 1703 2994 0 0 1831 3424 145 115 94 100 88 100 6449 4697 .499 2.002 1.758 2.177 1.962 1.572 52 277 1.953 .97 80 4790 7920 58 66 322 330 0 4633 545 4087 1.903 3391 2845 .526 1.671 .928 .74
19 1667 674 991 604 676 70 1657 666 1014 617 666 62 0 0 507 194 154 112 81 34 75 21 746 728 9.657 .104 .093 .196 .199 3.464 32 159 .135 .31 60 4940 7920 59 65 338 344 0 641 574 67 .098 633 59 10.162 .088 -3.345 -3.499
20 2273 2005 976 574 1297 1431 2216 1694 982 582 1240 1120 0 0 880 885 122 110 96 98 94 98 2728 2360 .906 1.103 .903 1.166 1.137 1.576 52 335 1.055 .94 90 5080 7910 56 65 350 359 0 1905 545 1360 1.048 1610 1064 .954 .858 .068 -.22

Total number of rows: 42624

Table truncated, full table size 9854 Kbytes.




Supplementary data files not provided
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