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Sample GSM67507 Query DataSets for GSM67507
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/2003-02/37427.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 2030 1532 786 453 1244 1079 2106 1538 798 466 1320 1085 0 0 471 394 143 129 94 98 94 96 2323 2405 1.153 .867 .822 .834 .859 1.377 52 266 .886 .9 80 2440 7760 42 50 87 95 0 1493 442 1052 .845 1499 1058 1.183 .801 -.242 -.32
2 2370 2703 787 472 1583 2231 2323 2515 791 489 1536 2043 0 0 922 1242 132 148 94 98 94 96 3814 3579 .71 1.409 1.33 1.357 1.352 1.505 52 244 1.41 .95 80 2580 7760 42 50 101 109 0 2635 460 2175 1.374 2451 1991 .728 1.296 .458 .375
3 4334 4774 812 488 3522 4286 4546 4981 825 501 3734 4493 0 0 1114 1425 137 142 100 100 100 100 7808 8227 .822 1.217 1.203 1.218 1.17 1.32 52 244 1.239 .97 80 2730 7760 42 50 116 124 0 4653 476 4178 1.186 4855 4379 .843 1.173 .246 .23
4 1695 892 805 466 890 426 1770 879 824 478 965 413 0 0 469 269 124 117 92 90 92 80 1316 1378 2.089 .479 .428 .458 .494 1.913 52 244 .486 .83 80 2870 7760 42 50 130 138 0 869 454 415 .467 857 403 2.143 .417 -1.1 -1.261
5 1716 1141 736 434 980 707 1894 1221 738 440 1158 787 0 0 615 376 141 119 86 88 82 84 1687 1945 1.386 .721 .68 .664 .631 1.504 52 256 .659 .9 80 3020 7770 43 51 145 153 0 1112 423 689 .703 1190 767 1.422 .662 -.508 -.594
6 4701 10060 706 440 3995 9620 4964 10717 730 445 4258 10277 0 0 1494 2684 134 116 96 100 94 100 13615 14535 .415 2.408 2.414 2.679 2.341 1.658 52 246 2.329 .97 80 3170 7770 43 51 160 168 0 9806 429 9377 2.347 10446 10017 .426 2.353 1.231 1.234
7 2011 1432 790 454 1221 978 2084 1443 798 459 1294 989 0 0 779 528 117 100 88 92 88 90 2199 2283 1.248 .801 .764 .747 .731 1.539 52 246 .737 .91 80 3310 7770 43 51 174 182 0 1396 443 953 .781 1407 964 1.281 .745 -.357 -.425
8 1766 965 770 446 996 519 1861 1046 780 452 1091 600 0 0 589 322 138 109 90 86 88 76 1515 1691 1.919 .521 .55 .479 .486 1.635 52 246 .502 .86 80 3460 7770 43 51 189 197 0 941 435 506 .508 1020 585 1.969 .536 -.977 -.9
9 4817 5948 813 453 4004 5495 4712 5431 818 468 3899 4978 0 0 2234 2902 146 126 92 98 90 98 9499 8877 .729 1.372 1.277 1.386 1.353 1.299 52 246 1.343 .98 80 3600 7770 43 51 203 211 0 5798 442 5356 1.338 5294 4852 .748 1.244 .42 .316
10 1070 679 788 463 282 216 940 555 803 469 152 92 0 0 563 359 136 126 53 44 34 32 498 244 1.306 .766 .605 .673 .595 3.546 52 246 .606 .73 80 3750 7770 43 51 218 226 0 662 451 211 .747 541 90 1.339 .59 -.422 -.761
11 2362 2018 779 475 1583 1543 2362 2134 802 473 1583 1659 0 0 947 799 167 113 90 96 90 94 3126 3242 1.026 .975 1.048 .895 .909 1.804 52 246 .944 .94 80 3890 7770 43 51 232 240 0 1967 463 1504 .95 2080 1617 1.053 1.022 -.074 .031
12 2270 1533 709 431 1561 1102 2355 1503 728 435 1646 1072 0 0 947 691 160 104 92 98 86 92 2663 2718 1.417 .706 .651 .676 .628 1.752 52 266 .689 .92 80 4040 7770 43 51 247 255 0 1494 420 1074 .688 1465 1045 1.453 .635 -.539 -.656
13 1701 1095 733 438 968 657 1671 1095 743 441 938 657 0 0 578 378 121 103 90 92 88 86 1625 1595 1.473 .679 .7 .609 .642 1.668 52 256 .624 .86 80 4190 7770 43 51 262 270 0 1067 427 640 .662 1067 640 1.512 .683 -.596 -.551
14 1685 897 804 466 881 431 1642 893 807 474 838 427 0 0 430 220 120 112 96 92 94 84 1312 1265 2.044 .489 .51 .455 .438 1.581 52 256 .457 .78 80 4330 7770 43 51 276 284 0 874 454 420 .477 870 416 2.097 .497 -1.068 -1.01
15 5234 21544 810 462 4424 21082 5904 23140 812 489 5094 22678 0 0 1632 6242 137 237 96 100 94 100 25506 27772 .21 4.765 4.452 4.851 4.619 1.262 52 256 4.708 .97 80 4480 7770 43 51 291 299 0 20999 450 20549 4.645 22555 22104 .215 4.339 2.216 2.117
16 1696 1146 729 450 967 696 1775 1225 755 473 1046 775 0 0 574 335 165 233 88 88 88 75 1663 1821 1.389 .72 .741 .658 .668 1.58 52 244 .647 .85 80 4620 7770 43 51 305 313 0 1117 439 678 .702 1194 755 1.425 .722 -.511 -.47
17 1305 783 748 451 557 332 812 491 761 449 64 40 0 0 2511 1776 152 96 46 40 38 21 889 104 1.678 .596 .625 .513 .553 2.698 52 254 .704 .98 80 4770 7770 43 51 320 328 0 763 440 324 .581 479 39 1.721 .609 -.783 -.715
18 2560 2859 786 453 1774 2406 2140 2003 782 456 1354 1550 0 0 1819 2424 125 100 76 90 73 84 4180 2904 .737 1.356 1.145 1.346 1.252 2.159 52 244 1.34 .97 80 4920 7770 43 51 335 343 0 2787 442 2345 1.322 1952 1511 .756 1.116 .403 .158
19 1084 588 797 449 287 139 936 518 798 459 139 69 0 0 434 228 137 107 50 44 38 25 426 208 2.065 .484 .496 .504 .58 3.753 52 244 .426 .62 80 5060 7770 43 51 349 357 0 573 438 135 .472 505 67 2.118 .484 -1.083 -1.047
20 2014 1858 796 450 1218 1408 1818 1756 802 463 1022 1306 0 0 782 820 146 114 94 98 90 96 2626 2328 .865 1.156 1.278 1.11 1.132 1.433 52 244 1.121 .9 80 5210 7770 43 51 364 372 0 1811 439 1372 1.127 1712 1273 .888 1.246 .172 .317

Total number of rows: 42624

Table truncated, full table size 9628 Kbytes.




Supplementary data files not provided
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