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Sample GSM67512 Query DataSets for GSM67512
Status Public on Aug 05, 2005
Title HSF1 +/+ Mouse Fibroblasts Heat Shock 0 hours #2 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 #2 mRNA
Organism Mus musculus
Characteristics HSF1 +/+ Mouse Fibroblasts Heat Shock 0 hours #2 mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37438.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 2408 969 543 171 1865 798 2587 940 549 178 2044 769 0 0 851 431 102 59 98 98 97 96 2663 2813 2.337 .428 .376 .401 .438 1.404 80 402 .437 .96 100 2110 7810 46 56 53 63 0 1501 265 1237 .663 1457 1192 1.508 .583 -.593 -.779
2 3670 3313 573 180 3097 3133 3807 3138 579 186 3234 2958 0 0 1821 1977 99 60 98 100 98 100 6230 6192 .989 1.012 .915 1.003 1.034 1.25 52 233 1.038 .99 80 2260 7810 47 55 69 77 0 5134 279 4855 1.568 4862 4584 .638 1.417 .649 .503
3 4585 3457 561 179 4024 3278 4653 3454 563 181 4092 3275 0 0 2257 2044 100 54 100 100 98 98 7302 7367 1.228 .815 .8 .791 .783 1.233 80 355 .845 .99 100 2400 7820 47 57 82 92 0 5357 277 5079 1.262 5352 5075 .792 1.24 .336 .311
4 1863 657 562 189 1301 468 1947 699 563 187 1385 510 0 0 801 305 118 56 88 86 86 82 1769 1895 2.78 .36 .368 .334 .359 1.479 52 314 .353 .93 90 2540 7810 46 55 96 105 0 1018 293 725 .557 1083 790 1.794 .571 -.843 -.809
5 2309 750 571 190 1738 560 2528 756 589 198 1957 566 0 0 765 252 168 78 94 96 94 94 2298 2523 3.104 .322 .289 .326 .335 1.392 52 318 .323 .93 90 2690 7800 45 54 111 120 0 1162 294 868 .499 1171 877 2.003 .448 -1.002 -1.158
6 4862 7572 575 183 4287 7389 4993 7506 588 192 4418 7323 0 0 2252 3852 135 70 100 100 100 100 11676 11741 .58 1.724 1.658 1.74 1.767 1.177 80 391 1.729 .99 100 2840 7810 46 56 126 136 0 11733 284 11450 2.671 11631 11347 .374 2.568 1.417 1.361
7 2884 1478 571 179 2313 1299 3088 1575 575 181 2517 1396 0 0 1145 662 102 57 96 100 96 98 3612 3913 1.781 .562 .555 .554 .555 1.333 52 257 .556 .96 80 2990 7810 47 55 142 150 0 2290 277 2013 .87 2441 2163 1.149 .859 -.201 -.219
8 2126 893 572 184 1554 709 2167 823 576 186 1595 639 0 0 847 405 104 63 96 96 94 96 2263 2234 2.192 .456 .401 .445 .446 1.642 52 254 .437 .93 80 3130 7810 47 55 156 164 0 1384 285 1099 .707 1275 990 1.415 .621 -.5 -.688
9 5062 6158 576 184 4486 5974 3980 4549 577 184 3404 4365 0 0 3199 4224 106 59 98 100 97 98 10460 7769 .751 1.332 1.282 1.388 1.324 1.366 80 364 1.334 .99 100 3280 7810 46 56 170 180 0 9542 285 9257 2.064 7049 6764 .485 1.987 1.045 .991
10 903 428 572 181 331 247 684 282 581 189 112 101 0 0 519 365 104 62 53 63 40 40 578 213 1.34 .746 .902 .586 .621 3.404 52 292 .646 .83 90 3420 7800 45 54 184 193 0 663 280 383 1.156 437 157 .865 1.397 .21 .483
11 2498 2104 576 176 1922 1928 2728 2233 584 185 2152 2057 0 0 1133 1052 104 62 92 100 92 100 3850 4209 .997 1.003 .956 1.133 .983 2.054 52 328 .979 .95 90 3560 7810 46 55 198 207 0 3260 273 2988 1.554 3460 3187 .643 1.481 .636 .567
12 2661 1446 576 175 2085 1271 2526 1377 586 184 1950 1202 0 0 1229 691 108 62 94 98 92 98 3356 3152 1.64 .61 .616 .625 .6 1.375 52 342 .584 .96 90 3720 7810 46 55 214 223 0 2241 271 1969 .945 2134 1863 1.059 .955 -.082 -.066
13 2791 1336 585 184 2206 1152 2600 950 599 193 2015 766 0 0 1338 1253 145 74 100 100 100 100 3358 2781 1.915 .522 .38 .427 .466 1.606 32 218 .647 .91 70 3860 7800 46 53 229 236 0 2070 285 1785 .809 1472 1187 1.236 .589 -.305 -.764
14 2204 616 600 177 1604 439 2282 604 614 186 1682 427 0 0 468 177 136 64 100 100 100 93 2043 2109 3.654 .274 .254 .259 .26 1.562 32 204 .263 .88 70 4010 7800 46 53 244 251 0 955 274 680 .424 936 662 2.358 .393 -1.238 -1.346
15 3815 12495 589 179 3226 12316 3327 11550 597 185 2738 11371 0 0 1809 6617 116 61 97 100 97 100 15542 14109 .262 3.818 4.153 3.927 3.786 1.292 80 385 3.828 .99 100 4150 7810 46 56 257 267 0 19361 277 19084 5.916 17897 17620 .169 6.435 2.565 2.686
16 1772 697 579 174 1193 523 1668 675 580 181 1089 501 0 0 766 307 107 61 92 93 91 88 1716 1590 2.281 .438 .46 .42 .419 1.939 80 353 .408 .93 100 4300 7810 46 56 272 282 0 1080 270 810 .679 1046 776 1.472 .713 -.558 -.488
17 899 256 587 175 312 81 706 237 590 184 119 62 0 0 560 129 107 62 51 50 40 23 393 181 3.852 .26 .521 .223 .188 2.557 52 302 .164 .55 90 4440 7800 45 54 286 295 0 397 271 126 .402 367 96 2.486 .807 -1.314 -.309
18 3863 5204 592 182 3271 5022 3653 4649 603 196 3061 4467 0 0 2803 3774 117 94 87 100 87 100 8293 7528 .651 1.535 1.459 1.62 1.537 1.299 32 199 1.435 .99 70 4590 7810 47 54 302 309 0 8064 282 7782 2.379 7204 6922 .42 2.261 1.25 1.177
19 837 229 588 187 249 42 727 222 596 194 139 35 0 0 438 88 120 79 51 28 38 7 291 174 5.929 .169 .252 .156 .153 3.5 52 352 .132 .43 90 4730 7800 45 54 315 324 0 355 290 65 .261 344 54 3.826 .39 -1.936 -1.358
20 2004 1449 611 187 1393 1262 1881 1259 616 189 1270 1072 0 0 1171 1022 114 61 90 96 84 96 2655 2342 1.104 .906 .844 .826 .859 1.523 52 257 .883 .97 80 4890 7810 47 55 332 340 0 2245 290 1956 1.404 1951 1661 .712 1.308 .489 .387

Total number of rows: 42624

Table truncated, full table size 9605 Kbytes.




Supplementary data files not provided
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