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Sample GSM90516 Query DataSets for GSM90516
Status Public on Jan 04, 2006
Title Puf4 IP (2)
Sample type RNA
 
Channel 1
Source name Puf4 tot. RNA extract (2)
Organism Saccharomyces cerevisiae
Characteristics Puf4 tot. RNA extract (2)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf4 RNA-IP (2)
Organism Saccharomyces cerevisiae
Characteristics Puf4 RNA-IP (2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36825.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
1 198 49 192 49 6 0 195 48 197 49 3 -1 0 0 30 8 48 9 7 12 0 1 6 2 null null null .266 .228 2.923 80 423 .11 .45 100 2730 16890 56 66 24 34 -50 339 339 0 null 332 -7 null null null null
2 204 52 201 51 3 1 191 50 239 58 -10 -1 0 0 54 10 139 25 1 2 1 0 4 -11 3 .333 null .228 .227 2.725 80 420 .178 .94 100 2900 16890 56 66 41 51 -50 359 352 7 2.304 346 -7 .434 null 1.204 null
3 207 54 205 53 2 1 199 52 248 60 -6 -1 0 0 41 9 139 24 1 0 0 0 3 -7 2 .5 null .283 .3 2.994 80 432 .137 .72 100 3070 16890 56 66 58 68 -50 373 366 7 3.456 359 -7 .289 null 1.789 null
4 209 53 204 52 5 1 205 54 220 56 1 2 0 0 35 8 73 15 2 3 0 0 6 3 5 .2 2 .277 .239 3.136 80 432 .131 .65 100 3250 16890 56 66 76 86 -50 366 359 7 1.382 373 14 .723 13.823 .467 3.789
5 219 52 202 53 17 -1 216 51 206 53 14 -2 0 0 41 9 37 8 21 12 5 3 16 12 null null null .258 .24 3.051 80 420 .115 .51 100 3420 16890 56 66 93 103 -50 359 366 -7 null 352 -14 null null null null
6 216 53 216 55 0 -2 215 53 248 59 -1 -2 0 0 30 8 91 16 0 2 0 0 -2 -3 null null null .334 .328 3.466 80 390 .147 .76 100 3590 16890 56 66 110 120 -50 366 380 -14 null 366 -14 null null null null
7 383 85 221 58 162 27 391 87 254 62 170 29 0 0 104 21 89 16 82 77 40 37 189 199 6 .167 .171 .171 .171 1.872 120 531 .167 .89 130 3750 16920 57 70 124 137 0 587 401 187 1.152 601 200 .868 1.179 .204 .238
8 412 91 212 56 200 35 408 87 233 59 196 31 0 0 94 20 67 13 96 92 77 68 235 227 5.714 .175 .158 .167 .172 1.694 80 405 .175 .89 110 3930 16910 57 68 143 154 0 629 387 242 1.21 601 214 .827 1.093 .274 .128
9 339 78 207 54 132 24 350 79 224 57 143 25 0 0 92 16 62 13 80 78 59 47 156 168 5.5 .182 .175 .182 .184 1.893 120 466 .167 .86 120 4100 16920 58 70 160 172 0 539 373 166 1.257 546 173 .796 1.208 .33 .273
10 1057 168 214 55 843 113 1004 153 233 58 790 98 0 0 326 50 64 14 100 100 100 98 956 888 7.46 .134 .124 .131 .13 1.232 80 449 .133 .97 110 4270 16890 55 66 177 188 0 1161 380 781 .926 1057 677 1.079 .857 -.11 -.222
11 382 88 218 56 164 32 387 88 233 59 169 32 0 0 140 26 69 13 79 78 65 62 196 201 5.125 .195 .189 .202 .197 1.658 120 473 .168 .88 120 4440 16920 58 70 194 206 0 608 387 221 1.349 608 221 .742 1.309 .431 .388
12 387 88 226 58 161 30 396 87 249 63 170 29 0 0 74 14 83 17 86 85 52 33 191 199 5.367 .186 .171 .181 .187 1.551 80 399 .175 .89 110 4610 16910 57 68 211 222 0 608 401 207 1.288 601 200 .776 1.179 .365 .238
13 2672 466 232 57 2440 409 2753 472 245 61 2521 415 0 0 996 172 72 14 98 98 97 97 2849 2936 5.966 .168 .165 .17 .168 1.203 120 542 .166 .99 120 4790 16890 55 67 229 241 0 3221 394 2827 1.159 3262 2868 .863 1.138 .212 .186
14 39905 2939 230 58 39675 2881 39794 2876 262 65 39564 2818 0 0 8082 740 105 22 100 100 100 100 42556 42382 13.771 .073 .071 .072 .072 1.083 80 448 .073 1 110 4960 16880 54 65 246 257 0 20313 401 19912 .502 19878 19477 1.993 .492 -.995 -1.022
15 59023 9131 229 61 58794 9070 60866 9344 284 73 60637 9283 10 0 8725 1642 136 41 100 100 100 100 67864 69920 6.482 .154 .153 .154 .153 1.075 80 496 .155 1 110 5120 16880 54 65 262 273 0 63109 422 62688 1.066 64581 64160 .938 1.058 .093 .081
16 3284 442 210 57 3074 385 3126 411 247 67 2916 354 0 0 919 125 114 40 100 100 100 100 3459 3270 7.984 .125 .121 .124 .126 1.088 80 426 .125 .99 100 5300 16890 56 66 281 291 0 3055 394 2661 .866 2841 2447 1.155 .839 -.208 -.253
17 1379 263 198 54 1181 209 1341 258 204 55 1143 204 0 0 310 61 37 9 100 100 100 100 1390 1347 5.651 .177 .178 .176 .179 1.139 80 420 .177 .99 100 5470 16880 55 65 298 308 0 1818 373 1445 1.223 1783 1410 .818 1.234 .291 .303
18 15069 1850 198 55 14871 1795 14715 1810 204 55 14517 1755 0 0 2238 287 34 8 100 100 100 100 16666 16272 8.285 .121 .121 .121 .121 1.05 80 497 .12 1 110 5640 16880 54 65 314 325 0 12786 380 12406 .834 12510 12130 1.199 .836 -.261 -.259
19 2087 267 193 54 1894 213 1966 250 195 55 1773 196 0 0 530 61 31 8 100 100 100 100 2107 1969 8.892 .112 .111 .112 .112 1.112 80 412 .11 .99 100 5820 16880 55 65 333 343 0 1845 373 1472 .777 1728 1355 1.287 .764 -.364 -.388
20 2407 388 198 55 2209 333 2342 376 203 56 2144 321 0 0 587 97 37 8 100 100 100 100 2542 2465 6.634 .151 .15 .15 .149 1.12 80 462 .149 .99 110 5990 16880 54 65 349 360 0 2682 380 2302 1.042 2599 2219 .96 1.035 .059 .049

Total number of rows: 9984

Table truncated, full table size 2187 Kbytes.




Supplementary data files not provided
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