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Sample GSM90539 Query DataSets for GSM90539
Status Public on Jan 04, 2006
Title Puf2 IP (3)
Sample type RNA
 
Channel 1
Source name Puf2 tot. RNA extract (3)
Organism Saccharomyces cerevisiae
Characteristics Puf2 tot. RNA extract (3)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf2 RNA-IP (3)
Organism Saccharomyces cerevisiae
Characteristics Puf2 RNA-IP (3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36824.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)
GSE3968 Puf proteins, RNA co-immunopurification
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
1 139 60 136 59 3 1 137 59 137 60 1 0 0 0 21 11 20 10 21 17 5 6 4 1 3 .333 null .603 .557 2.809 80 468 .202 .3 100 2660 15550 62 72 17 27 -50 167 164 3 .928 164 0 1.078 null -.108 null
2 152 68 143 63 9 5 150 66 148 65 7 3 0 0 30 15 28 15 18 20 8 10 14 10 1.8 .556 .429 .492 .566 3.688 80 432 .263 .42 100 2830 15550 62 72 34 44 -50 189 175 14 1.546 184 8 .647 1.193 .629 .254
3 156 66 145 64 11 2 154 66 153 66 9 2 0 0 31 13 39 14 16 15 2 3 13 11 5.5 .182 .222 .49 .427 3.193 80 420 .248 .49 100 3000 15550 62 72 51 61 -50 184 178 6 .506 184 6 1.976 .618 -.983 -.693
4 259 113 163 72 96 41 254 105 238 106 91 33 0 0 100 41 228 105 10 8 1 0 137 124 2.341 .427 .363 .459 .422 2.233 80 427 .426 .96 100 3170 15540 61 71 68 78 -50 314 200 114 1.189 292 92 .841 1.009 .249 .013
5 738 338 236 108 502 230 426 177 332 149 190 69 0 0 839 379 372 167 31 25 12 21 732 259 2.183 .458 .363 .456 .447 1.589 32 215 .447 .98 70 3310 15560 64 71 83 90 -100 941 301 640 1.275 493 192 .784 1.011 .351 .015
6 168 76 181 79 -13 -3 156 74 237 102 -25 -5 0 0 56 24 290 120 1 1 0 0 -16 -30 null null null .383 .391 2.609 80 511 .393 .98 100 3510 15540 61 71 102 112 -50 211 220 -8 null 206 -14 null null null null
7 282 124 202 87 80 37 278 116 199 85 76 29 0 0 50 35 55 21 66 58 16 25 117 105 2.162 .463 .382 .391 .418 1.631 12 104 .406 .81 50 3680 15560 65 70 121 126 -100 345 242 103 1.287 323 81 .777 1.062 .364 .087
8 206 87 171 74 35 13 194 81 187 79 23 7 0 0 58 29 124 37 6 8 0 3 48 30 2.692 .371 .304 .427 .385 2.517 80 461 .276 .91 100 3860 15530 60 70 137 147 -50 242 206 36 1.034 225 19 .967 .847 .048 -.24
9 205 86 176 75 29 11 198 81 185 78 22 6 0 0 66 24 53 20 35 31 11 12 40 28 2.636 .379 .273 .328 .337 2.875 80 432 .33 .77 100 4030 15530 60 70 154 164 -50 239 209 31 1.056 225 17 .947 .759 .078 -.398
10 732 287 163 70 569 217 658 260 179 77 495 190 0 0 200 77 56 22 100 100 100 100 786 685 2.622 .381 .384 .38 .395 1.221 52 363 .363 .97 90 4190 15530 60 69 170 179 0 799 195 604 1.061 724 529 .942 1.068 .086 .095
11 212 85 173 73 39 12 201 81 181 76 28 8 0 0 75 24 49 19 31 30 21 11 51 36 3.25 .308 .286 .365 .339 2.672 80 451 .251 .7 100 4370 15520 59 69 188 198 -50 237 203 33 .856 225 22 1.168 .795 -.224 -.331
12 248 93 173 73 75 20 249 84 186 77 76 11 0 0 80 29 64 24 56 41 20 20 95 87 3.75 .267 .145 .297 .329 3.021 80 432 .303 .82 100 4540 15520 59 69 205 215 -50 259 203 56 .742 234 31 1.348 .403 -.43 -1.312
13 2074 833 177 71 1897 762 2077 866 188 75 1900 795 0 0 334 141 66 23 100 100 100 100 2659 2695 2.49 .402 .418 .399 .411 1.193 80 483 .396 .98 110 4710 15520 58 69 221 232 0 2318 198 2121 1.118 2410 2212 .895 1.164 .161 .22
14 11763 2557 181 71 11582 2486 12117 2605 196 76 11936 2534 0 0 2230 456 74 24 100 100 100 100 14068 14470 4.659 .215 .212 .215 .214 1.067 80 483 .211 1 110 4880 15520 58 69 238 249 0 7116 198 6918 .597 7249 7052 1.674 .591 -.743 -.759
15 52412 13845 170 72 52242 13773 53277 14109 201 81 53107 14037 0 0 7949 2587 77 32 100 100 100 100 66015 67144 3.793 .264 .264 .261 .266 1.116 80 502 .263 .99 110 5050 15510 57 68 255 266 0 38528 200 38328 .734 39263 39063 1.363 .736 -.447 -.443
16 3105 746 157 68 2948 678 3106 749 178 76 2949 681 0 0 455 95 67 30 100 100 100 100 3626 3630 4.348 .23 .231 .23 .228 1.087 80 415 .223 .99 100 5220 15520 59 69 273 283 0 2076 189 1887 .64 2084 1895 1.562 .643 -.644 -.638
17 834 279 142 63 692 216 837 283 145 64 695 220 0 0 97 38 24 10 100 100 100 100 908 915 3.204 .312 .317 .31 .32 1.174 80 432 .306 .98 100 5390 15510 58 68 290 300 0 776 175 601 .869 788 612 1.151 .881 -.203 -.183
18 5592 1493 140 63 5452 1430 5617 1555 145 64 5477 1492 0 0 1002 304 26 11 100 100 100 100 6882 6969 3.813 .262 .272 .26 .264 1.132 80 503 .262 .99 110 5560 15500 56 67 306 317 0 4155 175 3979 .73 4327 4152 1.37 .758 -.454 -.4
19 1303 382 142 62 1161 320 1321 381 143 64 1179 319 0 0 213 67 27 13 100 100 100 100 1481 1498 3.628 .276 .271 .275 .277 1.138 80 470 .271 .98 110 5740 15510 57 68 324 335 0 1063 173 891 .767 1060 888 1.304 .753 -.383 -.409
20 1468 595 142 63 1326 532 1399 582 143 64 1257 519 0 0 422 166 28 13 100 100 100 100 1858 1776 2.492 .401 .413 .402 .41 1.153 80 476 .392 .99 110 5900 15500 56 67 340 351 0 1656 175 1480 1.116 1620 1444 .896 1.149 .159 .2

Total number of rows: 9984

Table truncated, full table size 2169 Kbytes.




Supplementary data files not provided
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