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Sample GSM90542 Query DataSets for GSM90542
Status Public on Jan 04, 2006
Title Puf3_delta vs. WT, SC_glycerol (2)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA, SC_glycerol (2)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA, SC_glycerol (2)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf3_delta tot. RNA, SC_glycerol (2)
Organism Saccharomyces cerevisiae
Characteristics Puf3_delta tot. RNA, SC_glycerol (2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutant vs Wild-type, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47086.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 Jan 03, 2006
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 GPL3300
Series (2)
GSE3969 Puf3delta vs. wild type comparison
GSE4393 Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

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
1 256 145 237 123 19 22 234 127 270 254 -3 4 0 0 96 76 288 938 2 0 0 0 41 1 .864 1.158 null .792 .813 3.348 80 434 2.579 .92 100 2140 16970 52 62 25 35 -50 171 145 26 1.366 150 5 .732 null .449 null
2 267 153 221 121 46 32 247 132 255 228 26 11 0 0 112 93 284 885 5 0 1 0 78 37 1.438 .696 .423 .947 .949 3.531 80 442 8.535 .71 100 2320 16960 51 61 43 53 -50 180 143 38 .82 156 13 1.219 .499 -.286 -1.003
3 647 398 231 136 416 262 616 358 263 163 385 222 0 0 312 237 136 108 83 66 58 50 678 607 1.588 .63 .577 .479 .618 1.895 12 96 .695 .89 50 2500 17020 59 64 63 68 -100 469 160 309 .743 422 262 1.346 .68 -.429 -.556
4 253 140 222 120 31 20 240 127 224 127 18 7 0 0 91 68 52 49 22 22 10 7 51 25 1.55 .645 .389 .827 .824 4.083 80 478 .807 .56 100 2660 16960 51 61 77 87 -50 165 142 24 .761 150 8 1.314 .459 -.394 -1.125
5 298 161 252 128 46 33 260 136 308 137 8 8 0 0 139 102 219 58 8 21 1 15 79 16 1.394 .717 1 .932 .894 5.135 80 450 .603 .65 100 2830 16960 51 61 94 104 -50 190 151 39 .846 160 9 1.182 1.179 -.241 .238
6 343 178 236 126 107 52 258 135 239 131 22 9 0 0 278 147 71 54 25 28 16 17 159 31 2.058 .486 .409 .847 .8 2.972 80 450 .62 .8 100 3000 16960 51 61 111 121 -50 210 149 61 .573 159 11 1.745 .482 -.803 -1.052
7 327 190 232 129 95 61 260 145 232 134 28 16 0 0 237 162 62 51 33 20 16 15 156 44 1.557 .642 .571 .757 .659 3.223 80 462 .682 .79 100 3170 16960 51 61 128 138 -50 224 152 72 .757 171 19 1.321 .674 -.401 -.569
8 394 228 244 131 150 97 289 145 245 134 45 14 0 0 361 276 54 51 42 32 22 20 247 59 1.546 .647 .311 .61 .671 2.669 80 451 .742 .9 100 3350 16960 51 61 146 156 -50 269 154 114 .763 171 17 1.311 .367 -.391 -1.447
9 341 196 243 127 98 69 273 163 258 134 30 36 0 0 230 144 98 53 22 35 15 20 167 66 1.42 .704 1.2 .936 .838 3.444 80 415 .591 .74 100 3520 16960 51 61 163 173 -50 231 150 81 .83 192 42 1.204 1.415 -.268 .501
10 399 224 248 131 151 93 281 172 249 139 33 41 0 0 325 185 57 51 37 47 23 25 244 74 1.624 .616 1.242 1.079 .753 3.261 80 472 .563 .86 100 3690 16960 51 61 180 190 -50 264 154 110 .726 203 48 1.377 1.465 -.461 .551
11 394 243 239 134 155 109 300 165 237 140 61 31 0 0 283 192 69 55 45 43 25 31 264 92 1.422 .703 .508 .608 .643 4.6 80 472 .701 .8 100 3860 16960 51 61 197 207 -50 287 158 129 .829 195 37 1.206 .599 -.27 -.739
12 436 265 225 138 211 127 285 172 236 144 60 34 0 0 437 303 77 55 46 36 23 25 338 94 1.661 .602 .567 .678 .627 3.409 80 471 .684 .91 100 4030 16960 51 61 214 224 -50 313 163 150 .71 203 40 1.409 .668 -.494 -.581
13 1769 1345 227 132 1542 1213 1835 1371 232 144 1608 1239 0 0 319 305 90 64 100 100 100 100 2755 2847 1.271 .787 .771 .778 .811 1.271 80 526 .79 .96 110 4210 16970 51 62 231 242 0 1586 156 1430 .928 1617 1461 1.078 .909 -.108 -.138
14 8971 8833 232 142 8739 8691 9291 9149 253 174 9059 9007 0 0 1414 1697 129 147 100 100 100 100 17430 18066 1.006 .995 .994 .987 1.002 1.106 80 498 1.001 .99 110 4380 16970 51 62 248 259 0 10417 167 10249 1.173 10789 10622 .853 1.173 .23 .23
15 8612 15648 226 136 8386 15512 8939 16558 239 171 8713 16422 0 0 1829 3466 123 152 100 100 100 100 23898 25135 .541 1.85 1.885 1.838 1.836 1.109 80 528 1.866 .99 110 4560 16960 50 61 266 277 0 18454 160 18293 2.181 19527 19367 .458 2.223 1.125 1.152
16 2187 2055 223 141 1964 1914 2182 2058 253 175 1959 1917 0 0 411 351 223 169 100 100 100 100 3878 3876 1.026 .975 .979 .978 .951 1.228 52 332 .955 .97 90 4720 16960 51 60 283 292 0 2423 166 2257 1.149 2427 2261 .87 1.154 .201 .207
17 851 573 238 145 613 428 995 611 279 198 757 466 0 0 477 339 287 301 70 63 61 32 1041 1223 1.432 .698 .616 .585 .658 2.083 120 567 .693 .91 120 4890 16970 51 63 299 311 0 676 171 505 .823 721 550 1.214 .726 -.28 -.462
18 1682 2197 248 150 1434 2047 1878 2320 273 206 1630 2170 0 0 595 815 270 304 91 93 90 93 3481 3800 .701 1.427 1.331 1.401 1.368 1.687 80 504 1.361 .96 110 5070 16960 50 61 317 328 0 2591 177 2414 1.683 2736 2559 .594 1.57 .751 .651
19 1172 861 244 150 928 711 1188 863 304 208 944 713 0 0 206 225 386 263 100 98 76 80 1639 1657 1.305 .766 .755 .743 .743 1.359 52 352 .781 .93 90 5250 16940 49 58 336 345 0 1015 177 838 .904 1018 841 1.107 .891 -.146 -.167
20 949 840 243 156 706 684 974 840 287 186 731 684 0 0 653 608 315 214 66 68 60 63 1390 1415 1.032 .969 .936 .789 .867 1.817 80 497 .799 .94 110 5410 16950 49 60 351 362 0 991 184 807 1.143 991 807 .875 1.103 .192 .142

Total number of rows: 9984

Table truncated, full table size 2282 Kbytes.




Supplementary data files not provided
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