NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90526 Query DataSets for GSM90526
Status Public on Jan 04, 2006
Title Puf5 IP (2)
Sample type RNA
 
Channel 1
Source name Puf5 tot. RNA extract (2)
Organism Saccharomyces cerevisiae
Characteristics Puf5 tot. RNA extract (2)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf5 RNA-IP (2)
Organism Saccharomyces cerevisiae
Characteristics Puf5 RNA-IP (2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34717.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 GPL3269
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
1 674 123 58 28 616 95 694 128 59 28 636 100 0 0 108 40 12 8 100 92 100 92 711 736 6.484 .154 .157 .161 .166 1.303 52 355 .155 .89 90 2040 17850 38 47 35 44 0 724 165 559 .907 753 588 1.102 .925 -.141 -.113
2 22771 3309 56 30 22715 3279 21752 3837 58 31 21696 3807 0 0 18925 2766 12 8 100 92 100 89 25994 25503 6.927 .144 .175 .144 .144 2.371 120 580 .137 .94 120 2210 17850 37 49 51 63 0 19465 176 19288 .849 22571 22394 1.178 1.032 -.236 .046
3 48633 8162 57 29 48576 8133 58350 9337 59 30 58293 9308 13 0 19614 3022 11 9 100 100 100 100 56709 67601 5.973 .167 .16 .176 .163 2.183 80 434 .158 .95 100 2390 17850 38 48 70 80 0 48012 171 47841 .985 54924 54753 1.015 .939 -.022 -.09
4 2171 340 55 27 2116 313 2350 374 56 29 2295 347 0 0 616 134 10 8 100 93 100 91 2429 2642 6.76 .148 .151 .143 .157 1.663 80 440 .146 .93 100 2570 17840 37 47 88 98 0 2000 159 1841 .87 2200 2041 1.149 .889 -.201 -.169
5 1473 223 56 29 1417 194 1504 235 56 30 1448 206 0 0 423 89 9 8 100 92 100 92 1611 1654 7.304 .137 .142 .141 .152 1.741 80 440 .131 .89 100 2740 17840 37 47 105 115 0 1312 171 1141 .805 1382 1212 1.242 .837 -.312 -.257
6 12836 1747 57 26 12779 1721 13905 1966 63 27 13848 1940 0 0 4723 812 33 9 100 100 100 97 14500 15788 7.425 .135 .14 .133 .142 1.654 80 441 .133 .94 100 2910 17840 37 47 122 132 0 10276 153 10124 .792 11565 11412 1.262 .824 -.336 -.279
7 1688 262 57 29 1631 233 1854 290 58 30 1797 261 0 0 501 93 21 7 100 98 100 98 1864 2058 7 .143 .145 .137 .144 1.736 80 452 .139 .94 100 3090 17840 37 47 140 150 0 1541 171 1371 .84 1706 1535 1.19 .854 -.251 -.227
8 1130 182 55 26 1075 156 1130 177 56 26 1075 151 0 0 284 45 9 7 100 100 100 100 1231 1226 6.891 .145 .14 .143 .138 1.275 52 363 .139 .95 90 3260 17830 36 45 157 166 0 1071 153 918 .854 1041 888 1.171 .826 -.228 -.275
9 936 193 56 28 880 165 967 195 57 29 911 167 0 0 165 30 9 8 100 100 100 100 1045 1078 5.333 .188 .183 .188 .185 1.216 52 379 .178 .95 90 3430 17830 36 45 174 183 0 1135 165 971 1.103 1147 982 .907 1.078 .141 .109
10 532 102 56 28 476 74 566 104 56 28 510 76 0 0 172 37 9 8 100 95 100 92 550 586 6.432 .155 .149 .149 .149 1.565 80 474 .155 .92 100 3610 17830 36 46 192 202 0 600 165 435 .914 612 447 1.094 .877 -.129 -.19
11 999 201 55 26 944 175 1037 216 56 26 982 190 0 0 329 76 9 7 100 93 100 93 1119 1172 5.394 .185 .193 .18 .189 1.504 80 440 .185 .95 100 3790 17830 36 46 210 220 0 1182 153 1029 1.09 1271 1118 .917 1.138 .125 .187
12 1475 257 55 29 1420 228 1586 287 58 29 1531 258 0 0 494 96 15 8 100 98 100 97 1648 1789 6.228 .161 .169 .151 .165 1.629 80 476 .16 .94 110 3960 17820 34 45 226 237 0 1512 171 1341 .944 1688 1518 1.059 .991 -.082 -.013
13 1225 212 57 26 1168 186 1353 235 70 28 1296 209 0 0 775 88 142 12 91 93 85 90 1354 1505 6.28 .159 .161 .178 .171 1.949 80 439 .136 .85 100 4120 17830 36 46 243 253 0 1247 153 1094 .937 1382 1229 1.068 .949 -.094 -.076
14 11439 9996 56 29 11383 9967 12636 10869 76 36 12580 10840 0 0 4059 3662 146 42 100 100 100 100 21350 23420 1.142 .876 .862 .853 .902 2.032 80 511 .874 .95 110 4300 17830 35 46 260 271 0 58800 171 58629 5.151 63935 63765 .194 5.069 2.365 2.342
15 1179 3637 55 26 1124 3611 1373 4302 60 29 1318 4276 0 0 504 1797 33 21 100 100 100 100 4735 5594 .311 3.213 3.244 3.033 3.268 1.75 80 466 3.472 .94 100 4480 17820 35 45 279 289 0 21394 153 21241 18.898 25306 25153 .053 19.084 4.24 4.254
16 1033 226 56 27 977 199 1088 246 58 28 1032 219 0 0 232 67 12 8 100 98 100 96 1176 1251 4.91 .204 .212 .185 .214 2.039 52 362 .19 .91 90 4650 17820 35 44 296 305 0 1329 159 1171 1.198 1447 1288 .835 1.248 .261 .32
17 748 151 59 29 689 122 741 151 62 29 682 122 0 0 131 23 14 7 100 100 100 100 811 804 5.648 .177 .179 .176 .18 1.274 52 379 .161 .93 90 4820 17820 35 44 313 322 0 888 171 718 1.042 888 718 .96 1.052 .059 .074
18 1184 219 54 27 1130 192 1304 234 58 28 1250 207 0 0 517 102 25 8 100 92 100 90 1322 1457 5.885 .17 .166 .158 .166 2.095 80 474 .164 .93 100 5000 17820 35 45 331 341 0 1288 159 1129 .999 1376 1218 1.001 .974 -.001 -.038
19 1923 334 55 28 1868 306 2035 389 64 29 1980 361 0 0 782 135 42 9 100 98 100 95 2174 2341 6.105 .164 .182 .15 .166 1.825 80 474 .158 .95 100 5180 17820 35 45 349 359 0 1965 165 1800 .964 2288 2124 1.038 1.072 -.053 .101
20 427 96 56 27 371 69 432 100 56 35 376 73 0 0 79 22 8 53 100 75 100 3 440 449 5.377 .186 .194 .186 .184 1.494 52 368 .165 .6 90 5360 17820 35 44 367 376 0 565 159 406 1.094 588 429 .914 1.142 .13 .192

Total number of rows: 10752

Table truncated, full table size 2270 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap