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Sample GSM67503 Query DataSets for GSM67503
Status Public on Aug 05, 2005
Title HSF1 +/+ Mouse Fibroblasts Heat Shock 1 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 1 hours mRNA
Organism Mus musculus
Characteristics HSF1 +/+ Mouse Fibroblasts Heat Shock 1 hours mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37434.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 2451 965 622 196 1829 769 2608 990 641 227 1986 794 0 0 744 368 164 128 96 96 95 91 2598 2780 2.378 .42 .4 .4 .397 1.488 80 393 .415 .9 100 2220 7660 31 41 64 74 0 1644 334 1310 .716 1687 1353 1.396 .681 -.481 -.554
2 3668 2433 664 197 3004 2236 3763 2438 663 207 3099 2241 0 0 1469 1012 123 82 98 100 98 100 5240 5340 1.343 .744 .723 .818 .767 1.831 52 277 .724 .96 90 2360 7650 30 39 78 87 0 4145 336 3810 1.268 4154 3818 .788 1.232 .343 .301
3 4889 4428 658 193 4231 4235 5176 4623 684 204 4518 4430 0 0 1566 1687 341 84 100 100 100 100 8466 8948 .999 1.001 .981 .995 .994 1.239 80 379 1.006 .97 100 2510 7660 31 41 93 103 0 7545 329 7216 1.705 7877 7548 .586 1.671 .77 .74
4 2272 687 658 188 1614 499 2281 693 689 196 1623 505 0 0 546 240 414 74 96 96 92 92 2113 2128 3.234 .309 .311 .288 .331 1.756 52 254 .252 .81 80 2660 7650 31 39 109 117 0 1171 320 850 .527 1181 860 1.898 .53 -.925 -.916
5 2576 872 663 189 1913 683 2704 846 663 199 2041 657 0 0 564 311 146 88 100 98 100 97 2596 2698 2.801 .357 .322 .328 .33 1.558 80 352 .364 .9 100 2810 7660 31 41 123 133 0 1486 322 1164 .608 1441 1119 1.644 .548 -.717 -.867
6 5964 7956 660 192 5304 7764 6364 8372 669 202 5704 8180 0 0 1889 2616 126 86 100 100 100 100 13068 13884 .683 1.464 1.434 1.494 1.467 1.262 80 374 1.461 .98 110 2940 7660 30 41 135 146 0 13556 327 13229 2.494 14265 13937 .401 2.443 1.319 1.289
7 3189 1633 668 203 2521 1430 3435 1748 677 207 2767 1545 0 0 1019 525 123 71 98 100 94 100 3951 4312 1.763 .567 .558 .599 .549 1.472 52 302 .547 .95 90 3090 7650 30 39 151 160 0 2782 346 2436 .966 2978 2632 1.035 .951 -.049 -.072
8 2474 1127 678 198 1796 929 2600 1137 689 205 1922 939 0 0 787 467 158 69 96 100 92 98 2725 2861 1.933 .517 .489 .534 .542 1.92 52 285 .504 .93 90 3240 7660 31 40 166 175 0 1920 337 1583 .881 1937 1600 1.135 .832 -.182 -.265
9 6030 5833 657 195 5373 5638 5415 5217 671 205 4758 5022 0 0 3094 3295 170 75 100 100 100 100 11011 9780 .953 1.049 1.055 1.053 1.063 1.335 80 386 1.057 .98 100 3380 7650 30 40 180 190 0 9939 332 9606 1.788 8889 8557 .559 1.798 .838 .847
10 1613 547 673 198 940 349 1472 412 691 208 799 214 0 0 810 323 159 82 84 75 71 71 1289 1013 2.693 .371 .268 .326 .346 1.962 32 140 .336 .85 60 3530 7680 35 41 197 203 0 932 337 595 .633 702 365 1.581 .456 -.661 -1.132
11 3070 2490 677 194 2393 2296 3200 2215 694 202 2523 2021 0 0 1249 1196 121 68 98 100 98 100 4689 4544 1.042 .959 .801 .995 .965 1.384 52 324 .954 .96 90 3670 7650 30 39 209 218 0 4243 331 3912 1.635 3774 3443 .612 1.365 .709 .449
12 3072 2002 677 196 2395 1806 2844 1751 700 204 2167 1555 0 0 1555 1184 159 72 96 100 95 98 4201 3722 1.326 .754 .718 .763 .73 1.455 80 386 .756 .97 100 3820 7660 31 41 224 234 0 3411 334 3077 1.285 2983 2649 .778 1.223 .362 .29
13 2076 843 657 196 1419 647 2135 876 682 203 1478 680 0 0 972 453 177 73 88 90 82 84 2066 2158 2.193 .456 .46 .4 .432 1.557 52 301 .424 .9 90 3970 7650 30 39 239 248 0 1436 334 1102 .777 1493 1159 1.287 .784 -.364 -.351
14 2177 696 689 195 1488 501 2072 687 699 207 1383 492 0 0 717 289 152 73 98 92 94 92 1989 1875 2.97 .337 .356 .317 .323 1.641 52 276 .33 .89 90 4110 7650 30 39 253 262 0 1186 332 854 .574 1171 838 1.743 .606 -.802 -.722
15 4916 13136 675 197 4241 12939 4911 13137 695 210 4236 12940 0 0 2302 6576 172 74 98 100 95 100 17180 17176 .328 3.051 3.055 3.2 3.025 1.329 80 341 3.042 .98 100 4250 7660 31 41 267 277 0 22382 336 22046 5.198 22383 22048 .192 5.205 2.378 2.38
16 2026 750 656 202 1370 548 1951 685 690 207 1295 483 0 0 769 353 200 74 93 95 90 88 1918 1778 2.5 .4 .373 .362 .378 1.723 80 371 .397 .91 100 4400 7650 30 40 282 292 0 1278 344 934 .682 1167 823 1.467 .635 -.553 -.654
17 1524 319 687 206 837 113 1288 316 705 204 601 110 0 0 618 105 203 68 93 62 71 37 950 711 7.407 .135 .183 .168 .161 2.855 32 154 .104 .46 60 4550 7660 33 39 299 305 0 544 351 193 .23 538 187 4.347 .312 -2.12 -1.681
18 3654 3529 679 204 2975 3325 2081 2078 726 203 1402 1874 0 0 3177 3451 258 72 84 100 73 98 6300 3276 .895 1.118 1.337 1.152 1.112 1.44 52 257 1.098 .97 80 4690 7650 31 39 312 320 0 6013 348 5665 1.904 3541 3193 .525 2.277 .929 1.187
19 1020 243 694 191 326 52 758 236 740 200 64 45 0 0 600 86 291 68 38 38 23 15 378 109 6.269 .16 .703 .221 .194 4.411 52 329 .096 .42 90 4830 7640 29 38 325 334 0 414 325 89 .272 402 77 3.679 1.198 -1.879 .261
20 2203 1227 663 206 1540 1021 2087 1024 696 213 1424 818 0 0 1071 741 241 68 86 96 84 94 2561 2242 1.508 .663 .574 .605 .644 1.848 52 358 .621 .89 90 4990 7650 30 39 341 350 0 2091 351 1740 1.13 1745 1394 .885 .979 .176 -.031

Total number of rows: 42624

Table truncated, full table size 9743 Kbytes.




Supplementary data files not provided
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