NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM67505 Query DataSets for GSM67505
Status Public on Aug 05, 2005
Title HSF1 -/- Mouse Fibroblasts Heat Shock 8 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 8 hours mRNA
Organism Mus musculus
Characteristics HSF1 -/- Mouse Fibroblasts Heat Shock 8 hours mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37419.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
1 992 599 318 211 674 388 1036 611 321 218 718 400 0 0 259 185 52 62 100 98 97 90 1062 1118 1.737 .576 .557 .565 .582 1.496 80 390 .577 .88 100 2230 8290 56 66 50 60 0 727 256 471 .699 741 485 1.431 .676 -.517 -.565
2 1036 903 319 211 717 692 1025 884 324 215 706 673 0 0 391 407 52 59 100 97 98 92 1409 1379 1.036 .965 .953 .901 .951 1.607 80 304 .986 .94 100 2380 8290 56 66 65 75 0 1096 256 840 1.171 1073 817 .854 1.157 .228 .21
3 1334 3326 312 210 1022 3116 1346 3517 313 212 1034 3307 0 0 397 1179 53 59 100 100 100 100 4138 4341 .328 3.049 3.198 3.089 3.062 1.271 80 378 3.073 .98 110 2530 8290 55 66 79 90 0 4036 255 3782 3.7 4268 4013 .27 3.881 1.888 1.957
4 770 402 317 210 453 192 746 397 314 212 429 187 0 0 237 119 52 60 97 83 90 75 645 616 2.359 .424 .436 .433 .455 2.107 80 332 .419 .8 100 2680 8290 56 66 95 105 0 488 255 233 .514 482 227 1.944 .529 -.959 -.919
5 928 498 315 211 613 287 998 496 316 216 683 285 0 0 215 138 50 59 98 97 98 88 900 968 2.136 .468 .417 .439 .45 1.752 80 334 .469 .84 110 2820 8290 55 66 108 119 0 604 256 348 .568 602 346 1.76 .506 -.816 -.982
6 1320 1591 310 210 1010 1381 1288 1596 316 216 978 1386 0 0 673 919 53 57 90 95 87 90 2391 2364 .731 1.367 1.417 1.429 1.37 1.637 120 395 1.378 .98 120 2960 8300 56 68 122 134 0 1931 255 1676 1.659 1937 1682 .603 1.72 .731 .782
7 1084 649 318 218 766 431 1090 645 326 220 772 427 0 0 256 158 58 57 100 98 100 98 1197 1199 1.777 .563 .553 .549 .546 1.382 52 283 .553 .9 90 3110 8290 56 65 138 147 0 788 265 523 .683 783 518 1.464 .671 -.55 -.575
8 952 565 310 218 642 347 973 547 317 219 663 329 0 0 190 161 53 58 100 98 100 92 989 992 1.85 .54 .496 .497 .523 1.562 52 302 .565 .85 90 3260 8290 56 65 153 162 0 686 265 421 .656 664 399 1.525 .602 -.608 -.732
9 2157 1956 309 210 1848 1746 2148 1894 312 215 1839 1684 0 0 999 874 49 59 100 100 98 100 3594 3523 1.058 .945 .916 .979 .965 1.328 80 388 .923 .98 110 3410 8300 56 67 167 178 0 2374 255 2119 1.147 2299 2044 .872 1.111 .197 .152
10 676 372 322 212 354 160 598 355 323 216 276 143 0 0 236 156 54 57 100 65 93 59 514 419 2.213 .452 .518 .374 .392 2.309 32 184 .474 .68 70 3540 8310 59 66 182 189 0 451 257 194 .549 431 174 1.823 .629 -.866 -.669
11 952 568 322 214 630 354 856 516 325 216 534 302 0 0 445 265 57 56 97 88 93 83 984 836 1.78 .562 .566 .551 .579 1.825 80 365 .554 .92 100 3700 8290 56 66 197 207 0 689 260 430 .682 626 367 1.466 .686 -.552 -.543
12 817 1651 314 214 503 1437 744 1549 319 218 430 1335 0 0 331 928 55 60 95 98 90 97 1940 1765 .35 2.857 3.105 2.966 2.911 1.648 80 327 2.882 .97 100 3840 8290 56 66 211 221 0 2004 260 1744 3.467 1880 1620 .288 3.768 1.794 1.914
13 858 565 321 211 537 354 840 559 326 217 519 348 0 0 230 205 57 58 98 90 96 88 891 867 1.517 .659 .671 .611 .67 1.721 52 264 .688 .87 90 3990 8290 56 65 226 235 0 686 256 430 .8 678 422 1.25 .814 -.322 -.297
14 769 393 319 212 450 181 742 366 320 219 423 154 0 0 242 138 53 59 96 78 90 60 631 577 2.486 .402 .364 .381 .409 1.917 80 321 .424 .8 100 4130 8290 56 66 240 250 0 477 257 220 .488 444 187 2.049 .442 -1.035 -1.178
15 1393 2033 308 216 1085 1817 1251 1961 312 223 943 1745 0 0 884 1399 53 62 86 91 85 86 2902 2688 .597 1.675 1.85 1.627 1.687 1.746 120 402 1.65 .98 120 4290 8300 56 68 255 267 0 2467 262 2205 2.032 2380 2118 .492 2.246 1.023 1.167
16 850 426 313 219 537 207 867 432 317 229 554 213 0 0 248 141 54 81 98 80 98 60 744 767 2.594 .385 .384 .354 .4 1.79 80 314 .407 .81 100 4430 8290 56 66 270 280 0 517 266 251 .468 524 258 2.138 .467 -1.096 -1.1
17 511 271 319 222 192 49 462 262 324 224 143 40 0 0 212 92 62 58 63 44 55 25 241 183 3.918 .255 .28 .514 .39 3.632 52 304 .26 .43 90 4580 8290 56 65 285 294 0 329 269 59 .31 318 49 3.229 .339 -1.691 -1.559
18 1978 1254 316 219 1662 1035 1911 1253 319 220 1595 1034 0 0 943 565 59 61 100 100 100 100 2697 2629 1.606 .623 .648 .634 .638 1.281 32 199 .606 .97 70 4720 8300 58 65 300 307 0 1522 266 1256 .756 1521 1255 1.323 .787 -.404 -.346
19 503 255 313 209 190 46 443 235 310 215 130 26 0 0 184 81 66 64 67 30 50 17 236 156 4.13 .242 .2 .356 .412 3.018 52 349 .279 .39 90 4870 8290 56 65 314 323 0 309 254 56 .294 285 32 3.404 .243 -1.767 -2.043
20 997 571 326 216 671 355 1108 574 330 225 782 358 0 0 398 220 57 60 98 94 94 82 1026 1140 1.89 .529 .458 .516 .509 1.772 52 312 .52 .89 90 5020 8290 56 65 329 338 0 693 262 431 .642 697 434 1.557 .556 -.639 -.848

Total number of rows: 42624

Table truncated, full table size 9439 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap