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Sample GSM90517 Query DataSets for GSM90517
Status Public on Jan 04, 2006
Title BY4741 mock (2)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA extract (2)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA extract (2)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BY4741 RNA-IP (2)
Organism Saccharomyces cerevisiae
Characteristics BY4741 RNA-IP (2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36817.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
1 180 37 176 40 4 -3 175 37 181 40 -1 -3 0 0 35 5 41 5 16 6 5 0 1 -4 null null null .179 .179 2.747 80 455 .024 .15 100 2710 16690 36 46 22 32 -50 962 1040 -78 null 962 -78 null null null null
2 190 38 187 40 3 -2 184 39 194 40 -3 -1 0 0 38 5 48 5 16 12 0 0 1 -4 null null null .182 .17 3.249 80 432 .025 .23 100 2890 16690 36 46 40 50 -50 988 1040 -52 null 1014 -26 null null null null
3 197 38 192 41 5 -3 189 38 201 41 -3 -3 0 0 42 5 46 6 13 5 3 0 2 -6 null null null .175 .2 2.749 80 420 .028 .22 100 3060 16690 36 46 57 67 -50 988 1066 -78 null 988 -78 null null null null
4 194 39 194 41 0 -2 191 40 201 41 -3 -1 0 0 44 5 44 6 16 3 6 1 -2 -4 null null null .173 .14 3.672 80 420 .029 .2 100 3230 16690 36 46 74 84 -50 1014 1066 -52 null 1040 -26 null null null null
5 210 41 194 42 16 -1 204 41 202 42 10 -1 0 0 51 5 46 5 21 12 10 1 15 9 null null null .142 .126 3.98 80 420 .027 .23 100 3400 16690 36 46 91 101 -50 1066 1092 -26 null 1066 -26 null null null null
6 216 42 201 43 15 -1 206 42 217 43 5 -1 0 0 47 6 71 6 15 7 0 1 14 4 null null null .155 .112 4.289 80 430 .032 .26 100 3570 16680 35 45 108 118 -50 1092 1118 -26 null 1092 -26 null null null null
7 230 43 208 43 22 0 217 42 221 44 9 -1 0 0 99 7 84 7 20 13 6 2 22 8 null null null .103 .093 2.796 80 430 .037 .5 100 3750 16680 35 45 126 136 -50 1118 1118 0 null 1092 -26 null null null null
8 258 44 208 43 50 1 252 43 215 43 44 0 0 0 76 6 79 6 33 20 6 3 51 44 50 .02 null .091 .081 2.861 80 406 .032 .37 100 3920 16680 35 45 143 153 -50 1144 1118 26 .52 1118 0 1.922 null -.943 null
9 246 43 196 43 50 0 236 42 209 43 40 -1 0 0 83 7 78 7 31 13 10 3 50 39 null null null .092 .094 3.12 80 432 .04 .48 100 4090 16680 35 45 160 170 -50 1118 1118 0 null 1092 -26 null null null null
10 1069 74 197 43 872 31 972 73 207 43 775 30 0 0 389 16 72 6 100 95 100 90 903 805 28.129 .036 .039 .034 .035 1.362 80 440 .035 .92 100 4260 16690 36 46 177 187 0 1925 1118 806 .925 1899 780 1.082 1.007 -.113 .01
11 276 44 210 43 66 1 258 45 207 43 48 2 0 0 102 6 77 6 33 22 8 5 67 50 66 .015 .042 .102 .09 2.891 80 464 .032 .43 100 4430 16680 35 45 194 204 -50 1144 1118 26 .394 1170 52 2.538 1.084 -1.343 .116
12 294 46 237 44 57 2 283 45 240 45 46 1 0 0 109 6 74 6 30 18 7 5 59 47 28.5 .035 .022 .087 .061 3.583 80 401 .031 .44 100 4600 16680 35 45 211 221 -50 1196 1144 52 .913 1170 26 1.096 .565 -.132 -.823
13 3351 163 228 44 3123 119 3552 174 237 45 3324 130 0 0 1120 48 76 6 99 98 98 95 3242 3454 26.244 .038 .039 .039 .039 1.329 120 539 .037 .97 120 4770 16690 35 47 227 239 0 4239 1144 3095 .991 4526 3381 1.009 1.017 -.013 .025
14 25458 768 245 47 25213 721 24689 734 260 47 24444 687 0 0 6692 167 86 7 100 100 100 100 25934 25131 34.969 .029 .028 .029 .029 1.12 80 402 .028 .99 100 4950 16680 35 45 246 256 0 19975 1222 18752 .744 19090 17868 1.345 .731 -.427 -.452
15 63767 5418 221 47 63546 5371 65535 5358 251 48 65314 5311 83 0 6032 948 95 10 100 100 100 100 68917 70625 11.831 .085 .081 .084 .083 1.145 80 501 .083 .98 110 5110 16670 33 44 261 272 0 140916 1222 139693 2.198 139355 138133 .455 2.115 1.136 1.081
16 2574 143 201 45 2373 98 2608 146 220 46 2407 101 0 0 815 36 70 9 100 100 100 98 2471 2508 24.214 .041 .042 .041 .04 1.212 80 511 .04 .97 110 5290 16680 34 45 279 290 0 3719 1170 2549 1.074 3797 2627 .931 1.091 .103 .126
17 1161 81 201 44 960 37 1219 85 207 44 1018 41 0 0 335 16 42 5 100 95 100 93 997 1059 25.946 .039 .04 .037 .039 1.352 80 497 .037 .93 110 5470 16680 34 45 297 308 0 2107 1144 962 1.002 2211 1066 .998 1.048 .003 .067
18 13429 555 199 43 13230 512 13364 554 201 43 13165 511 0 0 3004 112 43 5 100 100 100 100 13742 13676 25.84 .039 .039 .039 .039 1.067 80 497 .038 .99 110 5640 16670 33 44 314 325 0 14435 1118 13317 1.007 14409 13291 .994 1.01 .009 .014
19 1567 98 201 43 1366 55 1581 95 208 43 1380 52 0 0 533 27 56 5 100 100 100 98 1421 1432 24.836 .04 .038 .038 .041 1.397 80 491 .04 .95 110 5810 16670 33 44 331 342 0 2549 1118 1430 1.047 2471 1352 .955 .98 .067 -.029
20 2811 145 218 43 2593 102 2317 129 234 44 2099 86 0 0 1259 48 73 6 100 100 100 100 2695 2185 25.422 .039 .041 .04 .039 1.208 80 496 .038 .98 110 5990 16670 33 44 349 360 0 3771 1118 2653 1.023 3355 2237 .977 1.066 .033 .092

Total number of rows: 9984

Table truncated, full table size 2150 Kbytes.




Supplementary data files not provided
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