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Sample GSM67502 Query DataSets for GSM67502
Status Public on Aug 05, 2005
Title HSF1 -/- Mouse Fibroblasts Heat Shock 0.5 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 0.5 hours mRNA
Organism Mus musculus
Characteristics HSF1 -/- Mouse Fibroblasts Heat Shock 0.5 hours mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37425.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 2063 1508 660 375 1403 1133 2156 1541 671 378 1496 1166 0 0 599 392 117 88 94 98 94 98 2536 2662 1.238 .808 .779 .793 .779 1.329 52 336 .762 .94 90 2140 8040 69 78 56 65 0 1725 429 1296 .924 1763 1334 1.082 .892 -.114 -.165
2 2492 2801 694 385 1798 2416 2449 2698 715 395 1755 2313 0 0 989 1195 231 102 94 100 90 98 4214 4068 .744 1.344 1.318 1.323 1.319 1.31 52 300 1.303 .94 90 2290 8040 69 78 71 80 0 3205 441 2764 1.537 3087 2647 .65 1.508 .621 .593
3 3896 3972 705 394 3191 3578 3982 4085 714 403 3277 3691 0 0 1228 1210 118 101 96 100 96 100 6769 6968 .892 1.121 1.126 1.13 1.105 1.324 52 325 1.103 .97 90 2430 8040 69 78 85 94 0 4545 451 4094 1.283 4674 4223 .779 1.289 .359 .366
4 1413 748 692 401 721 347 1512 753 691 406 820 352 0 0 525 283 112 92 82 82 82 75 1068 1172 2.078 .481 .429 .472 .497 1.705 52 274 .45 .82 80 2580 8040 70 78 101 109 0 856 459 397 .551 862 403 1.816 .491 -.861 -1.026
5 1898 1033 751 409 1147 624 1977 1068 779 415 1226 659 0 0 786 284 244 97 92 95 87 91 1771 1885 1.838 .544 .538 .534 .531 1.565 80 367 .412 .8 100 2730 8050 70 80 115 125 0 1182 468 714 .622 1222 754 1.606 .615 -.684 -.701
6 3483 6324 740 399 2743 5925 3595 6466 753 415 2855 6067 0 0 1112 1905 165 98 96 100 96 100 8668 8922 .463 2.16 2.125 2.253 2.093 1.481 80 384 2.123 .97 110 2870 8050 69 80 128 139 0 7236 457 6779 2.472 7398 6942 .405 2.431 1.305 1.282
7 1785 1226 747 404 1038 822 1961 1268 758 420 1214 864 0 0 583 418 128 94 88 92 88 92 1860 2078 1.263 .792 .712 .718 .727 1.438 52 254 .745 .89 80 3020 8040 70 78 145 153 0 1403 462 941 .906 1451 989 1.104 .814 -.142 -.296
8 1631 830 872 456 759 374 1695 841 866 467 823 385 0 0 472 233 144 117 90 88 90 80 1133 1208 2.029 .493 .468 .443 .429 1.636 52 264 .432 .8 80 3170 8040 70 78 160 168 0 950 522 428 .564 962 441 1.774 .535 -.827 -.902
9 4493 5347 897 483 3596 4864 4710 5601 891 495 3813 5118 0 0 1551 1908 151 123 94 100 94 98 8460 8931 .739 1.353 1.342 1.364 1.336 1.246 52 301 1.314 .98 90 3320 8040 69 78 174 183 0 6118 553 5565 1.548 6409 5856 .646 1.536 .63 .619
10 1002 606 791 429 211 177 930 515 809 439 139 86 0 0 373 247 152 109 48 46 21 30 388 225 1.192 .839 .619 .578 .713 4.71 52 257 .527 .7 80 3460 8030 69 77 189 197 0 693 491 203 .96 589 98 1.042 .708 -.059 -.498
11 1899 1379 716 392 1183 987 1994 1355 729 394 1278 963 0 0 655 516 118 86 90 94 90 92 2170 2241 1.199 .834 .754 .811 .838 1.529 52 308 .809 .93 90 3600 8050 70 79 202 211 0 1578 449 1129 .955 1550 1102 1.048 .862 -.067 -.214
12 2446 1854 779 428 1667 1426 2492 1810 809 460 1713 1382 0 0 808 639 182 146 90 98 90 96 3093 3095 1.169 .855 .807 .876 .799 1.608 52 276 .831 .94 80 3750 8040 70 78 218 226 0 2121 490 1632 .979 2071 1581 1.022 .923 -.031 -.115
13 1570 918 952 542 618 376 1547 909 967 565 595 367 0 0 462 296 226 164 76 69 61 55 994 962 1.644 .608 .617 .589 .532 2.466 52 287 .578 .83 80 3900 8030 69 77 233 241 0 1050 620 430 .696 1040 420 1.436 .706 -.523 -.503
14 1567 790 884 491 683 299 1623 786 905 504 739 295 0 0 390 212 191 127 84 81 81 59 982 1034 2.284 .438 .399 .47 .466 2.561 32 199 .42 .76 70 4050 8040 70 77 248 255 0 904 562 342 .501 899 338 1.996 .457 -.997 -1.131
15 3153 8467 774 432 2379 8035 3253 8890 784 431 2479 8458 0 0 1249 3579 150 92 96 100 96 100 10414 10937 .296 3.377 3.412 3.49 3.309 1.366 80 378 3.357 .96 100 4190 8040 69 79 261 271 0 9688 494 9194 3.864 10172 9678 .259 3.904 1.95 1.965
16 1557 894 773 426 784 468 1706 932 778 431 933 506 0 0 551 302 126 84 84 90 84 84 1252 1439 1.675 .597 .542 .527 .563 1.795 52 244 .529 .86 80 4340 8040 70 78 277 285 0 1023 487 535 .683 1066 579 1.464 .621 -.55 -.688
17 962 439 771 420 191 19 851 442 772 422 80 22 0 0 375 132 124 86 38 30 30 11 210 102 10.053 .099 .275 .355 .305 3.693 52 259 .249 .48 80 4480 8030 69 77 291 299 0 502 481 22 .114 506 25 8.786 .315 -3.135 -1.668
18 2935 3421 728 378 2207 3043 3138 3390 727 393 2410 3012 0 0 1253 1393 116 95 93 96 93 96 5250 5422 .725 1.379 1.25 1.33 1.364 2.159 32 207 1.284 .93 70 4620 8040 70 77 305 312 0 3914 433 3482 1.578 3879 3446 .634 1.43 .658 .516
19 963 414 728 379 235 35 862 416 730 388 134 37 0 0 391 122 113 90 55 30 34 5 270 171 6.714 .149 .276 .459 .415 3.393 52 288 .166 .35 80 4770 8030 69 77 320 328 0 474 434 40 .17 476 42 5.868 .316 -2.553 -1.662
20 1733 1364 786 412 947 952 1675 1198 822 435 889 786 0 0 724 713 379 149 75 84 53 78 1899 1675 .995 1.005 .884 .912 .936 1.847 52 276 .575 .71 80 4920 8030 69 77 335 343 0 1561 471 1089 1.15 1371 899 .869 1.012 .202 .017

Total number of rows: 42624

Table truncated, full table size 9632 Kbytes.




Supplementary data files not provided
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