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Sample GSM90519 Query DataSets for GSM90519
Status Public on Jan 04, 2006
Title Puf4 IP (4)
Sample type RNA
 
Channel 1
Source name Puf4 tot. RNA extract (4)
Organism Saccharomyces cerevisiae
Characteristics Puf4 tot. RNA extract (4)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf4 RNA-IP (4)
Organism Saccharomyces cerevisiae
Characteristics Puf4 RNA-IP (4)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36827.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
1 160 49 148 49 12 0 157 48 166 52 9 -1 0 0 34 7 90 16 3 2 0 0 12 8 null null null .215 .188 3.187 80 443 .147 .64 100 2740 16790 46 56 25 35 -50 293 293 0 null 287 -6 null null null null
2 156 49 152 51 4 -2 151 48 172 54 -1 -3 0 0 32 7 93 17 0 0 0 0 2 -4 null null null .24 .189 3.548 80 400 .125 .6 100 2910 16790 46 56 42 52 -50 293 305 -12 null 287 -18 null null null null
3 195 55 161 53 34 2 169 52 167 53 8 -1 0 0 136 18 37 8 25 11 7 3 36 7 17 .059 null .293 .227 3.203 80 445 .123 .8 100 3080 16790 46 56 59 69 -50 329 317 12 .352 311 -6 2.843 null -1.508 null
4 233 63 177 57 56 6 229 62 423 131 52 5 0 0 34 10 979 370 0 0 0 0 62 57 9.333 .107 .096 .143 .125 3.158 32 231 .172 .96 70 3250 16800 48 55 77 84 -100 377 341 36 .641 371 30 1.561 .575 -.642 -.799
5 264 67 177 57 87 10 206 59 315 97 29 2 0 0 224 39 717 269 2 0 0 0 97 31 8.7 .115 .069 .239 .191 3.505 80 445 .151 .88 100 3420 16790 46 56 93 103 -50 401 341 60 .687 353 12 1.455 .412 -.541 -1.278
6 181 54 173 56 8 -2 174 53 199 60 1 -3 0 0 34 7 83 14 2 2 0 0 6 -2 null null null .339 .333 3.349 80 359 .138 .7 100 3590 16790 46 56 110 120 -50 323 335 -12 null 317 -18 null null null null
7 348 82 173 56 175 26 372 83 197 60 199 27 0 0 117 20 79 14 79 73 60 46 201 226 6.731 .149 .136 .149 .153 1.708 156 614 .146 .89 140 3740 16820 47 61 123 137 -100 490 335 155 .888 496 161 1.126 .811 -.171 -.302
8 326 77 173 57 153 20 322 76 188 59 149 19 0 0 79 12 56 11 90 76 75 38 173 168 7.65 .131 .128 .127 .128 1.767 120 498 .132 .8 130 3940 16810 46 59 143 156 -100 460 341 120 .782 454 114 1.279 .762 -.356 -.391
9 307 74 174 57 133 17 312 75 189 59 138 18 0 0 78 14 56 12 85 62 65 32 150 156 7.824 .128 .13 .146 .145 1.994 120 413 .148 .81 130 4110 16820 47 60 160 173 -100 442 341 102 .764 448 108 1.308 .78 -.388 -.359
10 843 154 174 57 669 97 935 155 193 59 761 98 0 0 429 66 64 12 85 86 85 82 766 859 6.897 .145 .129 .161 .147 1.767 120 471 .148 .98 120 4270 16780 44 56 177 189 0 921 341 580 .867 927 586 1.153 .77 -.206 -.377
11 359 83 174 57 185 26 355 83 195 60 181 26 0 0 102 17 68 14 89 80 67 40 211 207 7.115 .141 .144 .139 .14 1.642 120 492 .138 .85 130 4440 16810 46 59 193 206 -100 496 341 155 .84 496 155 1.19 .859 -.251 -.219
12 361 82 173 55 188 27 354 82 197 60 181 27 0 0 101 16 76 15 85 76 66 40 215 208 6.963 .144 .149 .146 .143 1.684 120 439 .142 .88 120 4620 16810 47 59 212 224 -100 490 329 161 .859 490 161 1.165 .892 -.22 -.165
13 4325 722 179 57 4146 665 4798 796 200 60 4619 739 0 0 1371 221 72 14 100 100 100 100 4811 5358 6.235 .16 .16 .16 .161 1.096 120 469 .16 1 120 4780 16790 45 57 228 240 0 4317 341 3976 .959 4759 4419 1.043 .957 -.06 -.064
14 29347 2507 183 59 29164 2448 32630 2807 221 64 32447 2748 0 0 12266 1018 104 17 100 100 100 100 31612 35195 11.913 .084 .085 .086 .084 1.157 120 485 .083 1 120 4960 16780 44 56 246 258 0 14990 353 14637 .502 16783 16431 1.993 .506 -.995 -.982
15 51532 10144 188 62 51344 10082 64809 11624 254 69 64621 11562 36 0 20613 4022 152 20 100 100 100 100 61426 76183 5.093 .196 .179 .204 .196 1.21 120 517 .195 .99 120 5130 16780 44 56 263 275 0 60652 371 60281 1.174 69501 69131 .852 1.07 .232 .097
16 3130 551 192 61 2938 490 3016 549 221 65 2824 488 0 0 526 69 90 16 100 100 100 100 3428 3312 5.996 .167 .173 .168 .17 1.075 80 463 .164 .99 110 5300 16780 44 55 280 291 0 3294 365 2930 .997 3283 2918 1.003 1.033 -.004 .047
17 1649 367 192 60 1457 307 1596 365 195 61 1404 305 0 0 378 72 39 8 100 100 100 100 1764 1709 4.746 .211 .217 .212 .209 1.09 80 489 .208 .99 110 5470 16770 43 54 297 308 0 2194 359 1836 1.26 2182 1824 .794 1.299 .333 .377
18 18752 2015 181 60 18571 1955 18870 2054 187 61 18689 1994 0 0 3118 333 35 8 100 100 100 100 20526 20683 9.499 .105 .107 .105 .105 1.035 80 488 .105 1 110 5640 16770 43 54 314 325 0 12048 359 11689 .629 12281 11922 1.589 .638 -.668 -.649
19 2270 365 178 60 2092 305 2239 354 182 61 2061 294 0 0 508 64 35 8 100 100 100 100 2397 2355 6.859 .146 .143 .147 .145 1.099 80 468 .143 .99 110 5810 16770 43 54 331 342 0 2182 359 1824 .872 2117 1758 1.147 .853 -.198 -.23
20 2770 500 186 63 2584 437 2592 449 194 64 2406 386 0 0 993 200 44 10 100 100 100 100 3021 2792 5.913 .169 .16 .165 .165 1.109 80 482 .174 .99 110 5980 16770 43 54 348 359 0 2990 377 2613 1.011 2685 2308 .989 .959 .016 -.06

Total number of rows: 9984

Table truncated, full table size 2153 Kbytes.




Supplementary data files not provided
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