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Sample GSM67504 Query DataSets for GSM67504
Status Public on Aug 05, 2005
Title HSF1 -/- Mouse Fibroblasts Heat Shock 0 hours #3 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 0 hours #3 mRNA
Organism Mus musculus
Characteristics HSF1 -/- Mouse Fibroblasts Heat Shock 0 hours #3 mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37426.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 1640 1210 598 328 1042 882 1757 1293 612 341 1159 965 0 0 469 341 137 102 95 98 93 95 1924 2124 1.181 .846 .833 .847 .846 1.47 80 387 .833 .93 100 2170 7820 47 57 59 69 0 1099 298 801 .769 1174 876 1.301 .756 -.379 -.403
2 2758 3123 623 341 2135 2782 2807 3154 625 345 2184 2813 0 0 917 1117 93 92 98 100 98 100 4917 4997 .767 1.303 1.288 1.374 1.308 1.427 52 277 1.291 .98 90 2310 7810 46 55 73 82 0 2837 310 2527 1.184 2865 2555 .845 1.17 .243 .226
3 3344 3755 604 331 2740 3424 3479 3973 610 340 2875 3642 0 0 1254 1471 87 89 100 100 100 100 6164 6517 .8 1.25 1.267 1.264 1.253 1.242 80 369 1.253 .97 100 2460 7820 47 57 88 98 0 3411 301 3110 1.135 3609 3308 .881 1.151 .183 .202
4 1512 712 621 314 891 398 1605 717 619 322 984 403 0 0 397 238 89 81 96 94 92 90 1289 1387 2.239 .447 .41 .474 .443 1.972 52 254 .458 .84 80 2610 7810 47 55 104 112 0 647 285 361 .406 651 366 2.465 .372 -1.301 -1.427
5 1835 1093 607 315 1228 778 1847 1110 609 322 1240 795 0 0 367 298 92 84 98 100 98 100 2006 2035 1.578 .634 .641 .635 .632 1.427 52 305 .643 .92 90 2750 7810 46 55 117 126 0 993 286 707 .575 1008 722 1.738 .582 -.797 -.78
6 5686 11068 608 325 5078 10743 6242 12073 620 336 5634 11748 0 0 1949 3748 103 103 100 100 100 100 15821 17382 .473 2.116 2.085 2.168 2.129 1.227 80 369 2.098 .98 100 2900 7820 47 57 132 142 0 10053 295 9758 1.922 10966 10670 .52 1.894 .942 .921
7 1910 1137 632 325 1278 812 1981 1141 645 339 1349 816 0 0 460 297 119 118 98 100 94 94 2090 2165 1.574 .635 .605 .629 .61 1.416 52 301 .632 .91 90 3050 7810 46 55 147 156 0 1033 295 738 .577 1036 741 1.733 .549 -.793 -.864
8 1601 855 640 331 961 524 1578 861 655 336 938 530 0 0 444 286 137 90 98 94 94 90 1485 1468 1.834 .545 .565 .528 .515 1.597 52 289 .525 .83 90 3200 7810 46 55 162 171 0 777 301 476 .495 782 481 2.019 .513 -1.014 -.962
9 4990 6753 629 331 4361 6422 5019 6710 642 339 4390 6379 0 0 1929 2991 158 82 100 100 100 100 10783 10769 .679 1.473 1.453 1.453 1.455 1.211 80 373 1.501 .98 100 3340 7810 46 56 176 186 0 6134 301 5833 1.338 6095 5794 .748 1.32 .42 .4
10 1124 794 643 322 481 472 1048 763 646 333 405 441 0 0 393 304 101 89 84 96 81 87 953 846 1.019 .981 1.089 .956 1.051 2.014 32 135 .892 .67 60 3480 7840 51 57 192 198 0 721 292 429 .891 693 401 1.122 .989 -.166 -.016
11 2153 1971 638 327 1515 1644 2124 2103 640 340 1486 1776 0 0 659 670 99 102 100 100 100 100 3159 3262 .922 1.085 1.195 1.11 1.12 1.382 52 331 1.076 .94 90 3620 7810 46 55 204 213 0 1790 297 1493 .986 1910 1613 1.015 1.086 -.021 .118
12 2215 1752 648 319 1567 1433 2206 1607 659 328 1558 1288 0 0 901 808 110 94 98 100 96 98 3000 2846 1.094 .914 .827 .933 .871 1.598 80 385 .908 .94 100 3780 7810 46 56 220 230 0 1591 290 1302 .831 1460 1170 1.204 .751 -.268 -.413
13 1593 877 636 319 957 558 1620 840 645 332 984 521 0 0 548 271 101 114 94 96 92 90 1515 1505 1.715 .583 .529 .605 .616 1.556 52 242 .547 .85 80 3920 7810 47 55 235 243 0 797 290 507 .53 763 473 1.888 .481 -.917 -1.056
14 1613 727 647 337 966 390 1638 732 651 340 991 395 0 0 295 173 109 85 100 94 100 90 1356 1386 2.477 .404 .399 .369 .401 1.716 52 254 .408 .81 80 4070 7810 47 55 250 258 0 660 306 354 .367 665 359 2.727 .362 -1.447 -1.466
15 5018 20294 645 339 4373 19955 5054 19981 651 359 4409 19642 0 0 1859 8200 116 145 100 100 100 100 24328 24051 .219 4.563 4.455 4.563 4.446 1.186 80 402 4.593 .99 110 4220 7810 45 56 263 274 0 18432 308 18125 4.145 18148 17840 .241 4.046 2.051 2.017
16 1665 1326 657 340 1008 986 1740 1357 653 347 1083 1017 0 0 332 349 99 93 100 100 100 98 1994 2100 1.022 .978 .939 .968 .987 1.301 52 288 .875 .87 90 4360 7810 46 55 278 287 0 1204 309 896 .888 1233 924 1.126 .853 -.171 -.23
17 888 454 662 351 226 103 778 387 675 361 116 36 0 0 322 255 164 101 44 34 28 19 329 152 2.194 .456 .31 .629 .544 3.43 52 257 .782 .63 80 4510 7800 46 54 294 302 0 412 319 94 .414 352 33 2.416 .282 -1.272 -1.827
18 3219 4363 659 354 2560 4009 2485 3385 751 394 1826 3031 0 0 2154 3215 669 267 73 100 55 98 6569 4857 .639 1.566 1.66 1.695 1.614 1.421 52 245 1.541 .98 80 4650 7820 48 56 308 316 0 3963 322 3641 1.422 3075 2753 .703 1.508 .508 .592
19 994 461 660 345 334 116 906 400 666 351 246 55 0 0 343 170 99 86 73 46 57 26 450 301 2.879 .347 .224 .365 .364 3.509 52 285 .294 .45 80 4800 7800 46 54 323 331 0 419 313 105 .315 363 50 3.17 .203 -1.665 -2.3
20 2233 2623 657 342 1576 2281 2200 2670 671 347 1543 2328 0 0 937 1320 108 89 98 100 92 98 3857 3871 .691 1.447 1.509 1.499 1.451 1.366 52 313 1.453 .97 90 4950 7810 46 55 337 346 0 2382 311 2072 1.315 2425 2114 .761 1.37 .395 .455

Total number of rows: 42624

Table truncated, full table size 9739 Kbytes.




Supplementary data files not provided
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