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Sample GSM90540 Query DataSets for GSM90540
Status Public on Jan 04, 2006
Title Puf3_delta vs. WT, SC_glycerol (3)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA, SC_glycerol (3)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA, SC_glycerol (3)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf3_delta tot. RNA, SC_glycerol (3)
Organism Saccharomyces cerevisiae
Characteristics Puf3_delta tot. RNA, SC_glycerol (3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutant vs Wild-type, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47301.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
1 226 164 189 116 37 48 199 130 217 139 10 14 0 0 94 109 126 91 8 13 5 8 85 24 .771 1.297 1.4 .969 1 4.613 80 479 .859 .66 100 2360 15870 38 48 35 45 -50 272 192 80 2.152 216 23 .465 2.322 1.106 1.216
2 220 162 186 116 34 46 191 105 219 138 5 -11 0 0 93 157 153 102 10 15 2 11 80 -6 .739 1.353 null 1.444 1.421 4.084 80 434 1.719 .74 100 2540 15870 38 48 53 63 -50 269 192 76 2.244 174 -18 .446 null 1.166 null
3 230 165 189 115 41 50 199 115 201 122 10 0 0 0 121 152 73 40 15 22 6 17 91 10 .82 1.22 null 1.122 1.075 3.217 80 408 1.169 .77 100 2710 15870 38 48 70 80 -50 274 191 83 2.023 191 0 .494 null 1.017 null
4 224 168 190 120 34 48 205 125 213 131 15 5 0 0 79 144 96 59 10 18 5 12 82 20 .708 1.412 .333 1.072 1.2 3.859 80 428 1.003 .7 100 2880 15870 38 48 87 97 -50 279 199 80 2.342 207 8 .427 .553 1.228 -.855
5 248 191 188 124 60 67 207 127 196 129 19 3 0 0 131 172 48 41 28 25 18 20 127 22 .896 1.117 .158 .951 1.074 3.774 80 428 1.282 .81 100 3050 15870 38 48 104 114 -50 317 206 111 1.852 211 5 .54 .262 .889 -1.933
6 226 182 194 127 32 55 196 131 204 136 2 4 0 0 108 139 59 50 20 22 12 17 87 6 .582 1.719 2 .989 1.054 2.885 80 440 1.285 .77 100 3220 15870 38 48 121 131 -50 302 211 91 2.851 217 7 .351 3.318 1.512 1.73
7 231 167 192 127 39 40 209 133 199 132 17 6 0 0 103 122 50 42 23 22 12 15 79 23 .975 1.026 .353 1.173 1.107 2.34 80 489 1.142 .77 100 3400 15870 38 48 139 149 -50 277 211 66 1.701 221 10 .588 .586 .767 -.772
8 631 595 210 148 421 447 492 605 230 159 282 457 0 0 407 383 67 71 91 91 66 66 868 739 .942 1.062 1.621 1.106 1.072 1.492 12 98 1.005 .95 50 3570 15910 44 49 158 163 0 987 246 742 1.761 1004 758 .568 2.688 .817 1.427
9 261 216 189 128 72 88 205 140 192 133 16 12 0 0 159 204 37 37 36 32 22 25 160 28 .818 1.222 .75 1.266 1.366 3.535 80 465 1.293 .86 100 3740 15870 38 48 173 183 -50 358 212 146 2.028 232 20 .493 1.244 1.02 .315
10 249 212 187 129 62 83 212 149 191 132 25 20 0 0 118 207 39 35 37 32 21 23 145 45 .747 1.339 .8 1.08 1.286 2.797 80 440 1.691 .82 100 3910 15870 38 48 190 200 -50 352 214 138 2.221 247 33 .45 1.327 1.151 .408
11 256 215 190 130 66 85 209 142 197 137 19 12 0 0 153 229 47 46 31 30 16 18 151 31 .776 1.288 .632 1.155 1.157 2.788 80 435 1.484 .85 100 4080 15870 38 48 207 217 -50 357 216 141 2.136 236 20 .468 1.048 1.095 .067
12 260 235 197 141 63 94 202 152 223 162 5 11 0 0 160 207 104 88 17 21 12 18 157 16 .67 1.492 2.2 1.446 1.398 3.605 80 407 1.155 .88 100 4260 15870 38 48 225 235 -50 390 234 156 2.475 252 18 .404 3.65 1.308 1.868
13 7914 4566 206 150 7708 4416 9578 5483 248 185 9372 5333 0 0 5069 2576 185 129 96 97 91 92 12124 14705 1.745 .573 .569 .649 .577 1.501 156 578 .541 .99 140 4430 15890 38 52 240 254 0 7575 249 7326 .95 9096 8847 1.052 .944 -.073 -.083
14 41939 35543 202 149 41737 35394 55732 42167 222 170 55530 42018 14 0 23875 19426 155 109 100 100 100 100 77131 97548 1.179 .848 .757 .9 .868 1.186 156 609 .835 .99 150 4610 15880 36 51 257 272 0 58963 247 58716 1.407 69952 69705 .711 1.255 .492 .328
15 32786 35444 201 149 32585 35295 19194 29604 243 212 18993 29455 33 37 28847 27518 281 379 100 100 100 100 67880 48448 .923 1.083 1.551 1.344 1.295 1.359 208 925 1.012 .99 170 4790 15900 37 54 274 291 0 58799 247 58552 1.797 49111 48864 .557 2.573 .846 1.363
16 14227 12683 206 153 14021 12530 14673 12492 312 308 14467 12339 0 0 2706 2396 451 608 100 100 100 100 26551 26806 1.119 .894 .853 .894 .904 1.07 80 342 .877 .99 100 4940 15870 38 48 293 303 -50 21040 254 20786 1.483 20723 20469 .675 1.415 .568 .501
17 2416 1570 206 146 2210 1424 2496 1632 218 160 2290 1486 0 0 779 402 65 73 100 100 100 100 3634 3776 1.552 .644 .649 .668 .637 1.253 120 577 .618 .97 130 5110 15880 37 50 308 321 0 2605 242 2362 1.069 2707 2465 .936 1.076 .096 .106
18 12603 8885 200 142 12403 8743 15138 10465 220 153 14938 10323 0 0 7105 4125 101 63 100 100 100 100 21146 25261 1.419 .705 .691 .785 .726 1.278 156 731 .664 .99 150 5290 15870 35 50 325 340 0 14740 236 14504 1.169 17361 17125 .855 1.146 .226 .197
19 3160 1948 200 142 2960 1806 3396 2031 223 155 3196 1889 0 0 1121 580 112 67 100 100 100 100 4766 5085 1.639 .61 .591 .632 .618 1.268 120 539 .587 .97 130 5460 15880 37 50 343 356 0 3232 236 2996 1.012 3369 3134 .988 .981 .017 -.028
20 4321 3660 198 142 4123 3518 4451 3648 209 150 4253 3506 0 0 1353 1004 65 49 100 100 100 100 7641 7759 1.172 .853 .824 .869 .857 1.222 80 442 .84 .98 110 5630 15870 37 48 361 372 0 6072 236 5836 1.415 6052 5816 .706 1.368 .501 .452

Total number of rows: 9984

Table truncated, full table size 2245 Kbytes.




Supplementary data files not provided
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