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Sample GSM90524 Query DataSets for GSM90524
Status Public on Jan 04, 2006
Title Puf1 IP (1)
Sample type RNA
 
Channel 1
Source name Puf1 tot. RNA extract (1)
Organism Saccharomyces cerevisiae
Characteristics Puf1 tot. RNA extract (1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf1 RNA-IP (1)
Organism Saccharomyces cerevisiae
Characteristics Puf1 RNA-IP (1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34714.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
1 805 108 67 26 738 82 831 108 68 25 764 82 0 0 152 43 12 6 100 92 100 92 820 846 9 .111 .107 .101 .103 1.645 52 376 .117 .9 90 1850 18300 57 66 44 53 0 771 186 586 .794 771 586 1.26 .767 -.333 -.383
2 45585 2529 71 27 45514 2502 50377 2903 74 27 50306 2876 1 0 16541 1079 19 9 100 100 100 100 48016 53182 18.191 .055 .057 .058 .058 1.557 80 462 .053 .92 100 2030 18300 57 67 62 72 0 18064 193 17871 .393 20736 20543 2.547 .408 -1.349 -1.292
3 30722 4680 70 28 30652 4652 32841 4995 72 28 32771 4967 0 0 11247 1712 17 9 100 100 100 100 35304 37738 6.589 .152 .152 .153 .153 1.787 80 440 .141 .92 100 2210 18300 57 67 80 90 0 33429 200 33229 1.084 35679 35479 .922 1.083 .116 .115
4 2464 315 65 25 2399 290 2399 337 66 25 2334 312 0 0 829 129 11 6 100 92 100 91 2689 2646 8.272 .121 .134 .116 .126 1.722 80 440 .115 .86 100 2380 18290 56 66 97 107 0 2250 179 2071 .863 2407 2229 1.158 .955 -.212 -.067
5 1601 217 64 27 1537 190 1545 218 65 27 1481 191 0 0 530 74 10 6 100 97 100 95 1727 1672 8.089 .124 .129 .128 .133 1.893 80 440 .11 .87 100 2550 18290 56 66 114 124 0 1550 193 1357 .883 1557 1364 1.133 .921 -.18 -.118
6 17100 2268 65 25 17035 2243 17395 2355 66 25 17330 2330 0 0 5333 749 10 6 100 100 100 100 19278 19660 7.595 .132 .134 .148 .136 1.82 80 499 .119 .89 110 2730 18290 55 66 131 142 0 16200 179 16021 .941 16821 16643 1.063 .96 -.088 -.058
7 2589 356 66 27 2523 329 2619 386 67 27 2553 359 0 0 601 125 10 6 100 93 100 93 2852 2912 7.669 .13 .141 .132 .144 1.466 80 440 .127 .92 100 2900 18280 55 65 149 159 0 2543 193 2350 .931 2757 2564 1.074 1.004 -.102 .006
8 1052 133 70 26 982 107 1113 130 70 26 1043 104 0 0 335 71 12 6 100 91 100 88 1089 1147 9.178 .109 .1 .106 .104 1.705 80 452 .108 .83 100 3080 18280 55 65 167 177 0 950 186 764 .778 929 743 1.285 .712 -.362 -.49
9 1732 261 70 27 1662 234 1709 266 72 27 1639 239 0 0 406 95 22 6 100 98 100 98 1896 1878 7.103 .141 .146 .133 .15 1.637 52 354 .128 .9 90 3240 18270 54 63 183 192 0 1864 193 1671 1.006 1900 1707 .994 1.042 .008 .059
10 633 75 69 27 564 48 623 72 71 27 554 45 0 0 294 30 20 6 100 92 97 90 612 599 11.75 .085 .081 .081 .084 1.563 80 466 .106 .72 100 3420 18270 54 64 201 211 0 536 193 343 .608 514 321 1.645 .58 -.718 -.785
11 2218 316 70 27 2148 289 2155 347 71 27 2085 320 0 0 677 116 12 6 100 98 100 97 2437 2405 7.433 .135 .153 .133 .149 1.79 80 444 .126 .9 100 3600 18270 54 64 219 229 0 2257 193 2064 .961 2479 2286 1.041 1.096 -.057 .133
12 3567 450 71 30 3496 420 3751 520 73 30 3680 490 0 0 889 185 12 7 100 93 100 91 3916 4170 8.324 .12 .133 .117 .135 1.667 80 428 .121 .91 100 3770 18260 53 63 236 246 0 3214 214 3000 .858 3714 3500 1.165 .951 -.221 -.072
13 1836 315 71 26 1765 289 1890 337 73 27 1819 311 0 0 584 103 12 6 100 98 100 98 2054 2130 6.107 .164 .171 .164 .166 2.106 80 428 .153 .92 100 3940 18270 54 64 253 263 0 2250 186 2064 1.17 2407 2221 .855 1.221 .226 .288
14 13795 1988 73 29 13722 1959 14263 2117 73 29 14190 2088 0 0 3922 668 11 6 100 100 100 98 15681 16278 7.005 .143 .147 .145 .147 1.652 80 450 .138 .94 100 4110 18270 54 64 270 280 0 14200 207 13993 1.02 15121 14914 .981 1.051 .028 .072
15 2702 366 73 27 2629 339 2570 372 73 28 2497 345 0 0 674 95 12 7 100 100 100 100 2968 2842 7.755 .129 .138 .126 .133 1.354 52 384 .126 .93 90 4290 18260 53 62 288 297 0 2614 193 2421 .921 2657 2464 1.086 .987 -.119 -.019
16 1430 207 74 28 1356 179 1467 220 75 29 1393 192 0 0 364 58 12 7 100 100 100 98 1535 1585 7.575 .132 .138 .123 .131 1.564 52 379 .127 .93 90 4460 18260 53 62 305 314 0 1479 200 1279 .943 1571 1371 1.061 .985 -.085 -.023
17 1175 174 75 29 1100 145 1147 184 76 30 1072 155 0 0 253 70 13 9 100 94 100 90 1245 1227 7.586 .132 .145 .12 .15 2.093 52 380 .13 .85 90 4630 18250 52 61 322 331 0 1243 207 1036 .942 1314 1107 1.062 1.033 -.087 .047
18 1276 234 75 27 1201 207 1289 223 75 27 1214 196 0 0 268 68 12 7 100 100 100 100 1408 1410 5.802 .172 .161 .169 .168 1.246 52 387 .163 .91 90 4800 18260 53 62 339 348 0 1671 193 1479 1.231 1593 1400 .812 1.153 .3 .206
19 3005 406 75 31 2930 375 2915 435 76 31 2840 404 0 0 541 123 12 7 100 100 100 100 3305 3244 7.813 .128 .142 .124 .148 1.577 52 386 .125 .89 90 4980 18250 52 61 357 366 0 2900 221 2679 .914 3107 2886 1.094 1.016 -.129 .023
20 720 152 75 26 645 126 671 152 76 27 596 126 0 0 222 52 12 6 100 100 100 100 771 722 5.119 .195 .211 .188 .198 1.329 52 384 .188 .94 90 5150 18250 52 61 374 383 0 1086 186 900 1.395 1086 900 .717 1.51 .481 .595

Total number of rows: 10752

Table truncated, full table size 2280 Kbytes.




Supplementary data files not provided
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