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Sample GSM67500 Query DataSets for GSM67500
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/2003-02/37424.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 1155 752 486 320 669 432 1195 782 493 322 709 462 0 0 305 200 127 72 95 96 91 93 1101 1171 1.549 .646 .652 .659 .634 1.585 80 391 .625 .88 100 2350 7830 53 63 45 55 0 722 307 415 .62 751 444 1.613 .626 -.689 -.676
2 1243 1214 495 328 748 886 1158 1128 513 328 663 800 0 0 540 579 178 70 85 95 81 93 1634 1463 .844 1.184 1.207 1.198 1.171 1.564 80 315 1.105 .88 100 2500 7830 53 63 60 70 0 1166 315 851 1.137 1083 768 .879 1.159 .186 .213
3 1969 2264 503 323 1466 1941 2102 2225 517 325 1599 1902 0 0 614 783 153 67 95 100 95 98 3407 3501 .755 1.324 1.189 1.42 1.315 1.789 80 342 1.334 .97 100 2640 7830 53 63 74 84 0 2174 310 1864 1.271 2137 1826 .787 1.142 .346 .192
4 1045 529 511 327 534 202 1073 569 516 328 562 242 0 0 368 165 82 69 84 75 80 69 736 804 2.644 .378 .431 .375 .427 2.128 52 277 .386 .76 90 2790 7830 53 62 89 98 0 508 314 194 .363 546 232 2.753 .414 -1.461 -1.274
5 1113 641 509 329 604 312 1197 661 509 329 688 332 0 0 314 192 80 69 93 88 90 82 916 1020 1.936 .517 .483 .486 .493 1.73 80 340 .535 .86 100 2930 7830 53 63 103 113 0 616 316 300 .496 635 319 2.016 .463 -1.011 -1.11
6 1958 4447 517 336 1441 4111 2068 4577 520 338 1551 4241 0 0 569 1312 82 71 97 100 97 98 5552 5792 .351 2.853 2.734 2.953 2.848 1.322 80 366 2.815 .97 100 3080 7830 53 63 118 128 0 4270 323 3948 2.74 4395 4073 .365 2.626 1.454 1.393
7 1132 759 530 343 602 416 1130 755 538 342 600 412 0 0 349 237 89 72 92 94 86 88 1018 1012 1.447 .691 .687 .734 .681 2.187 52 325 .646 .85 90 3230 7820 52 61 133 142 0 729 329 399 .664 725 396 1.507 .659 -.592 -.601
8 1155 654 542 346 613 308 1191 657 553 344 649 311 0 0 279 163 104 73 93 93 93 78 921 960 1.99 .502 .479 .505 .464 1.794 32 205 .489 .82 70 3380 7820 53 60 149 156 0 628 332 296 .482 631 299 2.073 .46 -1.051 -1.12
9 2550 3352 531 344 2019 3008 2255 3316 533 348 1724 2972 0 0 984 1388 95 78 98 100 98 98 5027 4696 .671 1.49 1.724 1.528 1.478 1.302 80 384 1.473 .98 100 3520 7830 53 63 162 172 0 3219 330 2889 1.431 3184 2854 .699 1.655 .517 .727
10 640 450 534 348 106 102 597 406 534 355 63 58 0 0 255 221 81 79 46 46 26 26 208 121 1.039 .962 .921 .645 .641 3.422 52 248 .754 .64 80 3670 7820 53 61 178 186 0 432 334 98 .924 390 56 1.082 .884 -.114 -.178
11 1267 1124 532 354 735 770 1244 1112 540 363 712 758 0 0 374 373 83 78 96 96 96 94 1505 1470 .955 1.048 1.065 .959 1.005 1.5 52 255 1.011 .92 80 3810 7820 53 61 192 200 0 1079 340 739 1.006 1068 728 .994 1.022 .009 .032
12 1310 1313 531 352 779 961 1204 1248 539 357 673 896 0 0 499 564 103 87 91 98 91 95 1740 1569 .811 1.234 1.331 1.251 1.247 1.678 80 362 1.21 .94 100 3960 7830 53 63 206 216 0 1261 338 923 1.185 1198 860 .844 1.278 .244 .354
13 1001 663 531 349 470 314 1032 650 539 347 501 301 0 0 313 234 111 72 88 84 78 73 784 802 1.497 .668 .601 .615 .668 1.815 52 300 .618 .79 90 4100 7820 52 61 220 229 0 637 335 302 .642 624 289 1.559 .577 -.64 -.794
14 1042 539 537 348 505 191 1076 547 543 345 539 199 0 0 343 155 92 70 92 80 86 71 696 738 2.644 .378 .369 .345 .377 2.646 52 235 .365 .73 80 4250 7820 53 61 236 244 0 518 334 183 .363 525 191 2.753 .355 -1.461 -1.496
15 1693 4462 551 355 1142 4107 1783 4903 553 360 1232 4548 0 0 675 1881 83 72 92 100 91 100 5249 5780 .278 3.596 3.692 3.739 3.563 1.435 80 356 3.47 .96 100 4390 7830 53 63 249 259 0 4285 341 3944 3.453 4708 4367 .29 3.545 1.788 1.826
16 1233 747 545 356 688 391 1190 748 553 357 645 392 0 0 546 245 86 72 92 88 88 86 1079 1037 1.76 .568 .608 .59 .635 1.836 52 256 .492 .84 80 4540 7820 53 61 265 273 0 717 342 375 .546 718 376 1.832 .584 -.874 -.777
17 684 359 550 350 134 9 624 345 557 353 74 -5 0 0 267 117 84 69 48 28 38 13 143 69 14.889 .067 null .603 .448 3.369 52 268 .291 .45 80 4690 7820 53 61 280 288 0 345 336 9 .064 331 -5 15.505 null -3.955 null
18 1873 2301 553 360 1320 1941 1724 2181 563 367 1171 1821 0 0 1055 1459 102 90 87 90 78 90 3261 2992 .68 1.47 1.555 1.572 1.433 1.536 32 214 1.413 .97 70 4830 7820 53 60 294 301 0 2210 346 1864 1.412 2094 1749 .708 1.493 .498 .579
19 699 349 539 357 160 -8 692 332 540 355 153 -25 0 0 282 107 84 76 59 21 44 7 152 128 null null null .368 .383 3.088 52 286 .293 .46 80 4980 7820 53 61 309 317 0 335 343 -8 null 319 -24 null null null null
20 1267 1072 558 380 709 692 1257 1031 569 383 699 651 0 0 372 387 99 91 96 96 93 90 1401 1350 1.025 .976 .931 .99 .861 1.6 32 164 .971 .89 60 5130 7820 54 60 325 331 0 1029 365 665 .937 990 625 1.067 .894 -.093 -.161

Total number of rows: 42624

Table truncated, full table size 9399 Kbytes.




Supplementary data files not provided
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