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Sample GSM75934 Query DataSets for GSM75934
Status Public on Sep 24, 2005
Title DES460 (wt) - mock irradiation - 60 min
Sample type RNA
 
Channel 1
Source name DES460 - asynchronous
Organism Saccharomyces cerevisiae
Characteristics DES460 - asynchronous
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name mock irradiated - 60 min
Organism Saccharomyces cerevisiae
Characteristics mock irradiated - 60 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, Gamma radiation
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5240.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 Sep 23, 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)
GSE3358 DNA damage responses and Mec1p

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1D_MEAN The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEAN Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; 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
PIX_RAT2_MEDIAN Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale
TOT_SPIX Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale
TOT_BPIX 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
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 User defined spot flag (default 0).; 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
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
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

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1B_MEAN CH2B_MEAN PERGTBCH1I_1SD PERGTBCH2I_1SD PIX_RAT2_MEDIAN TOT_SPIX TOT_BPIX REGR CORR TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN RAT1N_MEAN VALUE
1 2808 3993 1191 385 1617 3608 1194 392 52 67 1.828 225 990 2.25 .925 108 125 101 118 0 2679 258 2421 1.497 .668 .582
2 1246 428 1199 389 47 39 1230 397 6 8 .669 225 705 .182 .42 108 125 118 135 0 287 261 26 .553 1.808 -.854
3 2199 2190 1222 393 977 1797 1254 403 40 64 1.64 225 720 1.612 .908 108 125 135 152 0 1469 263 1206 1.234 .81 .304
4 1264 451 1207 392 57 59 1222 399 5 11 .67 225 709 .438 .671 108 125 153 170 0 302 263 39 .684 1.462 -.547
5 1439 883 1190 387 249 496 1204 397 8 40 1.228 225 720 1.408 .831 108 125 170 187 0 592 259 333 1.337 .748 .419
6 1218 436 1189 393 29 43 1196 400 5 9 .544 225 720 .392 .559 108 125 188 205 0 292 263 29 1 1 0
7 4284 8412 1237 392 3047 8020 1244 400 54 65 2.456 225 720 2.593 .958 108 125 205 222 0 5645 263 5382 1.766 .566 .821
8 1385 408 1324 396 61 12 1333 402 0 1 .478 225 720 .03 .066 108 125 223 240 0 273 265 8 .131 7.625 -2.931
9 1512 507 1408 408 104 99 1416 417 3 16 .569 225 720 .248 .521 108 125 240 257 0 340 273 67 .644 1.552 -.634
10 1421 444 1408 410 13 34 1416 422 0 6 .62 225 720 .071 .127 108 125 258 275 0 297 275 22 1.692 .591 .759
11 1369 406 1362 399 7 7 1411 436 0 4 .365 225 720 .424 .656 108 125 275 292 0 272 267 5 .714 1.4 -.485
12 1353 451 1332 396 21 55 1378 435 0 6 .575 225 720 .421 .641 108 125 293 310 0 302 265 37 1.762 .568 .817
13 1294 438 1300 401 null 37 1311 432 0 6 .73 225 720 .194 .216 108 125 310 327 0 293 269 24 null null null
14 1297 447 1291 412 6 35 1307 451 0 10 .643 225 720 .327 .34 108 125 328 345 0 300 276 24 4 .25 2
15 1287 423 1319 414 null 9 1326 439 0 5 .706 225 720 .218 .311 108 125 345 362 0 283 277 6 null null null
16 1287 394 1294 374 null 20 1306 390 0 3 .51 225 720 .084 .143 108 125 363 380 0 264 251 13 null null null
17 1265 379 1278 369 null 10 1285 381 0 4 .517 225 720 .056 .099 108 125 380 397 0 254 247 7 null null null
18 1285 382 1287 388 null null 1293 400 0 1 .511 225 720 .041 .076 108 125 398 415 0 256 260 null null null null
19 1268 393 1241 394 27 null 1245 408 0 5 .465 225 730 .064 .114 108 125 415 432 0 263 264 null null null null
20 2994 947 1162 371 1832 576 1175 400 6 12 .628 225 746 .276 .889 108 125 433 450 0 635 248 387 .211 4.734 -2.243

Total number of rows: 8064

Table truncated, full table size 946 Kbytes.




Supplementary data files not provided
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