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Sample GSM90534 Query DataSets for GSM90534
Status Public on Jan 04, 2006
Title Puf2 IP (2)
Sample type RNA
 
Channel 1
Source name Puf2 tot. RNA extract (2)
Organism Saccharomyces cerevisiae
Characteristics Puf2 tot. RNA extract (2)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf2 RNA-IP (2)
Organism Saccharomyces cerevisiae
Characteristics Puf2 RNA-IP (2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36822.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
1 169 53 176 54 -7 -1 164 53 231 66 -12 -1 0 0 24 8 149 33 0 0 0 0 -8 -13 null null null .274 .28 3.021 80 474 .184 .82 100 2710 17270 82 92 18 28 -50 259 264 -5 null 259 -5 null null null null
2 178 58 180 56 -2 2 171 57 208 61 -9 1 0 0 40 11 102 24 2 2 0 0 0 -8 null null null .328 .297 2.638 80 440 .191 .63 100 2890 17270 82 92 36 46 -50 284 274 10 null 279 5 null null null null
3 224 65 224 64 0 1 218 65 230 65 -6 1 0 0 52 12 60 14 10 12 3 1 1 -5 null null null .252 .241 3.184 80 432 .193 .72 100 3060 17260 81 91 53 63 -50 318 313 5 null 318 5 null null null null
4 233 66 230 65 3 1 227 64 238 66 -3 -1 0 0 37 10 54 13 10 12 0 1 4 -4 3 .333 null .235 .253 3.234 80 432 .177 .69 100 3230 17260 81 91 70 80 -50 323 318 5 1.632 313 -5 .613 null .707 null
5 186 55 183 55 3 0 186 53 184 55 3 -2 0 0 26 9 31 8 12 15 2 6 3 1 null null null .367 .323 3.331 80 440 .131 .43 100 3400 17260 81 91 87 97 -50 269 269 0 null 259 -10 null null null null
6 193 57 206 59 -13 -2 190 56 226 64 -16 -3 0 0 27 8 78 18 0 0 0 0 -15 -19 null null null .22 .226 3.056 80 440 .177 .75 100 3570 17260 81 91 104 114 -50 279 289 -10 null 274 -15 null null null null
7 379 99 322 83 57 16 375 97 345 89 53 14 0 0 71 19 172 34 7 17 0 0 73 67 3.563 .281 .264 .35 .325 2.577 80 432 .194 .79 100 3740 17250 80 90 121 131 -50 485 406 78 1.374 475 69 .728 1.293 .459 .371
8 465 120 410 100 55 20 462 119 403 101 52 19 0 0 67 19 100 24 27 43 0 5 75 71 2.75 .364 .365 .264 .282 2.878 80 420 .222 .82 100 3910 17250 80 90 138 148 -50 587 490 98 1.78 583 93 .562 1.789 .832 .839
9 492 122 445 108 47 14 460 114 490 116 15 6 0 0 120 31 211 39 8 21 2 3 61 21 3.357 .298 .4 .307 .302 2.523 80 440 .182 .9 100 4080 17250 80 90 155 165 -50 597 529 69 1.458 558 29 .686 1.958 .544 .97
10 855 204 261 71 594 133 864 201 342 86 603 130 0 0 252 49 241 44 92 96 63 78 727 733 4.466 .224 .216 .231 .23 1.286 80 439 .209 .96 100 4260 17250 80 90 173 183 0 999 348 651 1.096 984 636 .912 1.055 .133 .078
11 285 72 206 59 79 13 270 72 216 62 64 13 0 0 88 17 56 14 53 47 28 17 92 77 6.077 .165 .203 .237 .194 2.959 80 415 .177 .83 100 4420 17240 79 89 189 199 -50 352 289 64 .806 352 64 1.241 .994 -.312 -.008
12 269 71 202 58 67 13 250 68 217 62 48 10 0 0 75 17 60 14 43 42 20 18 80 58 5.154 .194 .208 .246 .213 2.591 80 425 .202 .83 100 4600 17240 79 89 207 217 -50 348 284 64 .95 333 49 1.053 1.02 -.074 .029
13 2781 577 233 62 2548 515 3035 650 241 63 2802 588 0 0 1156 236 62 12 99 100 98 100 3063 3390 4.948 .202 .21 .207 .203 1.238 120 544 .202 1 120 4770 17250 79 91 223 235 0 2825 304 2521 .99 3182 2879 1.011 1.027 -.015 .039
14 23220 2665 269 67 22951 2598 23082 2658 430 108 22813 2591 0 0 5351 620 643 181 100 100 100 100 25549 25404 8.834 .113 .114 .113 .113 1.042 80 464 .112 1 110 4940 17240 78 89 240 251 0 13047 328 12719 .554 13013 12685 1.804 .556 -.852 -.847
15 53993 9227 499 123 53494 9104 56992 9695 618 155 56493 9572 3 0 10904 1936 628 176 100 100 100 100 62598 66065 5.876 .17 .169 .17 .168 1.062 80 476 .169 1 110 5110 17230 77 88 257 268 0 45174 602 44571 .833 47465 46863 1.2 .83 -.263 -.27
16 2438 469 490 124 1948 345 2387 444 512 130 1897 320 0 0 723 130 213 46 98 100 97 97 2293 2217 5.646 .177 .169 .178 .178 1.142 80 470 .175 .99 110 5280 17240 78 89 274 285 0 2296 607 1689 .867 2174 1567 1.153 .826 -.206 -.276
17 1047 226 219 66 828 160 1012 218 268 77 793 152 0 0 275 53 137 30 100 100 98 98 988 945 5.175 .193 .192 .194 .193 1.145 80 428 .186 .99 100 5450 17230 78 88 292 302 0 1106 323 783 .946 1067 744 1.057 .938 -.08 -.092
18 8946 1623 192 61 8754 1562 8732 1561 220 65 8540 1500 0 0 2255 400 97 19 100 100 100 100 10316 10040 5.604 .178 .176 .179 .179 1.049 80 510 .176 1 110 5620 17230 77 88 308 319 0 7946 299 7647 .874 7642 7344 1.145 .86 -.195 -.218
19 1452 335 172 57 1280 278 1392 325 174 57 1220 268 0 0 395 81 37 9 100 100 100 100 1558 1488 4.604 .217 .22 .219 .221 1.09 80 477 .215 .99 110 5800 17230 77 88 326 337 0 1640 279 1361 1.063 1591 1312 .94 1.075 .089 .105
20 1569 356 153 53 1416 303 1610 362 156 54 1457 309 0 0 326 67 31 8 100 100 100 100 1719 1766 4.673 .214 .212 .215 .215 1.1 80 469 .212 .99 110 5970 17220 76 87 343 354 0 1743 259 1483 1.048 1772 1513 .955 1.038 .067 .054

Total number of rows: 9984

Table truncated, full table size 2174 Kbytes.




Supplementary data files not provided
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