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Sample GSM78366 Query DataSets for GSM78366
Status Public on Oct 15, 2005
Title Na 15min
Sample type RNA
 
Channel 1
Source name 0.8M NaCl 0min
Organism Saccharomyces cerevisiae
Characteristics 0.8M NaCl 0min
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 0.8M NaCl 15min
Organism Saccharomyces cerevisiae
Characteristics 0.8M NaCl 15min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: salt treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7758.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 14, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL2658
Series (1)
GSE3456 Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 2347 3328 350 359 1997 2969 null null 363 381 null null null null null null null null 100 100 null null null null .673 1.487 null null 1.459 null 80 459 1.464 .94 null null null 90 100 102 112 0 1912 206 1706 .854 null null 1.171 null -.227 null
2 323 421 324 350 -1 71 null null 336 396 null null null null null null null null 13 7 null null null null null null null null 1.873 null 80 455 .983 .33 null null null 88 98 119 129 -100 241 201 40 null null null null null null null
3 2465 4409 314 370 2151 4039 null null 326 419 null null null null null null null null 100 100 null null null null .533 1.878 null null 1.895 null 52 376 1.761 .94 null null null 89 98 136 145 0 2533 212 2321 1.079 null null .927 null .11 null
4 693 1157 322 383 371 774 null null 324 390 null null null null null null null null 93 96 null null null null .479 2.086 null null 1.977 null 32 176 1.636 .81 null null null 91 97 156 162 0 664 220 444 1.197 null null .836 null .259 null
5 1695 3430 351 436 1344 2994 null null 379 777 null null null null null null null null 88 71 null null null null .449 2.228 null null 1.945 null 52 328 3.222 .81 null null null 88 97 172 181 0 1971 250 1721 1.281 null null .781 null .357 null
6 579 1217 352 436 227 781 null null 401 756 null null null null null null null null 26 14 null null null null .291 3.441 null null 2.387 null 120 632 2.353 .6 null null null 86 98 184 196 -100 699 250 449 1.978 null null .506 null .984 null
7 505 631 333 400 172 231 null null 344 421 null null null null null null null null 73 44 null null null null .745 1.343 null null 1.273 null 52 312 .847 .51 null null null 89 97 210 218 0 362 229 133 .773 null null 1.293 null -.371 null
8 325 389 327 387 -2 2 null null 337 398 null null null null null null null null 11 8 null null null null null null null null .917 null 80 440 .362 .2 null null null 88 98 225 235 -100 223 222 1 null null null null null null null
9 355 421 335 388 20 33 null null 343 403 null null null null null null null null 17 8 null null null null .606 1.65 null null 2.222 null 80 452 .85 .31 null null null 88 98 242 252 -100 241 222 19 .95 null null 1.053 null -.074 null
10 347 393 337 393 10 null null null 339 406 null null null null null null null null 17 6 null null null null null null null null 2.667 null 80 452 .502 .23 null null null 88 98 260 270 -100 225 225 null null null null null null null null
11 379 470 333 387 46 83 null null 345 403 null null null null null null null null 12 22 null null null null .554 1.804 null null 1.21 null 80 452 .355 .16 null null null 88 98 277 287 -100 270 222 48 1.043 null null .958 null .061 null
12 344 417 337 389 7 28 null null 344 403 null null null null null null null null 15 22 null null null null .25 4 null null 1.191 null 80 452 .471 .26 null null null 88 98 295 305 -100 239 223 16 2.286 null null .438 null 1.193 null
13 347 396 335 398 12 -2 null null 343 412 null null null null null null null null 15 7 null null null null null null null null 1.742 null 80 444 .453 .23 null null null 87 97 312 322 -100 227 228 -1 null null null null null null null
14 356 415 344 421 12 -6 null null 352 435 null null null null null null null null 13 10 null null null null null null null null 1.714 null 80 466 .342 .17 null null null 87 97 330 340 -100 238 241 -3 null null null null null null null
15 356 456 368 440 -12 16 null null 378 456 null null null null null null null null 6 12 null null null null null null null null 1.277 null 80 454 .95 .51 null null null 87 97 348 358 -100 262 252 10 null null null null null null null
16 371 427 380 447 -9 -20 null null 392 465 null null null null null null null null 5 3 null null null null null null null null .845 null 80 444 .2 .13 null null null 87 97 365 375 -100 245 256 -11 null null null null null null null
17 371 468 355 423 16 45 null null 365 447 null null null null null null null null 18 13 null null null null .356 2.813 null null 1.742 null 80 466 .679 .26 null null null 87 97 383 393 -100 268 243 25 1.563 null null .64 null .644 null
18 408 622 355 427 53 195 null null 362 439 null null null null null null null null 21 19 null null null null .272 3.679 null null 1.989 null 52 289 2.336 .54 null null null 86 94 401 409 0 357 245 112 2.113 null null .473 null 1.079 null
19 377 489 369 437 8 52 null null 375 460 null null null null null null null null 12 23 null null null null .154 6.5 null null 1.52 null 80 455 .544 .21 null null null 87 97 418 428 -100 281 251 30 3.75 null null .267 null 1.907 null
20 387 453 366 456 21 -3 null null 372 478 null null null null null null null null 20 6 null null null null null null null null 1.163 null 80 454 .745 .32 null null null 87 97 435 445 -100 260 262 -2 null null null null null null null

Total number of rows: 8064

Table truncated, full table size 1978 Kbytes.




Supplementary data files not provided

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