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Sample GSM466866 Query DataSets for GSM466866
Status Public on Nov 10, 2009
Title Ribosome density experiment: mock 12 hrs. (5-12-08)
Sample type RNA
 
Channel 1
Source name aRNA generated from pooled mRNA associated with the light fractions of the polysome
Organism Homo sapiens
Characteristics source1: pooled mRNA associated with the light fractions of the polysome
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name aRNA generated from pooled mRNA associated with the heavy fractions of the polysome
Organism Homo sapiens
Characteristics source2: pooled mRNA associated with the heavy fractions of the polysome
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix
Description Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80365.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 Oct 30, 2009
Last update date Nov 06, 2009
Contact name Patrick O Brown
E-mail(s) pbrown@cmgm.stanford.edu
Organization name Stanford university school of medicine
Department Department of biochemistry
Street address Beckman Center b439
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL9497
Series (2)
GSE18836 Translation Profiling +/- miR-124
GSE18889 Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

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 2107 4061 129 144 1978 3917 2047 3974 136 153 1918 3830 0 0 247 368 58 58 100 100 100 100 5895 5748 .505 1.98 1.997 1.98 2.08 .17 52 424 1.95 1 80 1590 6550 189 197 109 117 0 6220 221 5999 3.033 6086 5866 .33 3.058 1.601 1.613
2 2172 4251 132 147 2040 4104 2163 4242 147 157 2031 4095 0 0 243 309 93 73 100 100 100 100 6144 6126 .497 2.012 2.016 2.02 2.08 .16 52 321 1.97 1 80 1740 6550 189 197 124 132 0 6511 225 6285 3.081 6497 6272 .325 3.088 1.623 1.627
3 18787 19977 135 149 18652 19828 21953 22552 150 163 21818 22403 0 0 6213 6466 94 78 100 100 100 100 38480 44221 .941 1.063 1.027 1.09 1.08 .21 69 283 1.06 1 90 1900 6550 188 197 139 148 0 30596 228 30367 1.628 34539 34311 .614 1.573 .703 .653
4 2252 4345 138 152 2114 4193 2208 4404 158 169 2070 4252 0 0 280 586 137 83 100 100 100 100 6307 6322 .504 1.983 2.054 1.98 2.04 .19 52 279 1.95 1 80 2050 6550 189 197 155 163 0 6655 233 6422 3.038 6745 6512 .329 3.146 1.603 1.653
5 8021 6272 139 156 7882 6116 8179 6552 185 218 8040 6396 0 0 657 727 296 385 100 100 100 100 13998 14436 1.289 .776 .796 .77 .79 .07 52 299 .8 1 80 2190 6550 189 197 169 177 0 9606 239 9367 1.188 10035 9796 .841 1.218 .249 .285
6 4962 26205 137 160 4825 26045 5771 30453 153 176 5634 30293 0 0 1918 9819 118 94 96 100 96 99 30870 35927 .185 5.398 5.377 5.63 5.56 1.57 69 292 5.24 1 90 2330 6540 187 196 182 191 0 40134 245 39889 8.267 46640 46395 .121 8.235 3.047 3.042
7 701 541 149 173 552 368 713 558 168 192 564 385 0 0 82 57 100 93 100 100 100 98 920 949 1.5 .667 .683 .66 .66 .08 52 341 .79 1 80 2500 6540 188 196 200 208 0 829 265 564 1.021 855 590 .979 1.045 .03 .064
8 21687 23408 148 173 21539 23235 22399 23603 259 203 22251 23430 0 0 2559 2631 1556 172 100 100 100 100 44774 45681 .927 1.079 1.053 1.07 1.08 .09 52 342 1.08 1 80 2660 6540 188 196 216 224 0 35850 265 35585 1.652 36149 35884 .605 1.613 .724 .689
9 57 62 142 162 -85 -100 56 52 243 186 -86 -110 0 0 8 29 1541 162 0 0 0 0 -185 -196 null null null 0 0 0 37 348 1.04 .99 70 2800 6540 188 195 230 237 -50 95 248 -153 null 80 -168 null null null null
10 147 148 141 160 6 -12 143 146 146 166 2 -14 0 0 25 25 36 48 8 5 3 0 -6 -12 null null null 2.18 1.04 1.92 37 343 1 .35 70 2950 6540 188 195 245 252 -50 227 245 -18 null 224 -21 null null null null
11 5345 10609 140 162 5205 10447 6000 12019 146 169 5860 11857 0 0 1743 3336 43 59 100 100 100 100 15652 17717 .498 2.007 2.023 2.3 2.08 1.5 69 337 1.99 1 90 3090 6530 186 195 258 267 0 16248 248 16000 3.074 18408 18160 .325 3.099 1.62 1.632
12 645 363 142 162 503 201 646 363 146 166 504 201 0 0 50 22 32 37 100 100 100 100 704 705 2.502 .4 .399 .39 .4 .06 52 329 .57 .99 80 3250 6540 188 196 275 283 0 556 248 308 .612 556 308 1.634 .611 -.708 -.711
13 11336 4419 143 161 11193 4258 11997 4680 151 167 11854 4519 0 0 2329 962 64 48 100 100 100 100 15451 16373 2.629 .38 .381 .38 .38 .1 52 289 .39 1 80 3400 6540 188 196 290 298 0 6768 247 6521 .583 7168 6921 1.716 .584 -.779 -.776
14 1489 1125 143 162 1346 963 1533 1148 151 169 1390 986 0 0 203 128 55 51 100 100 100 100 2309 2376 1.398 .715 .709 .71 .72 .07 52 323 .76 1 80 3550 6550 189 197 305 313 0 1723 248 1475 1.096 1758 1510 .913 1.086 .132 .12
15 46 41 149 169 -103 -128 46 40 160 180 -103 -129 0 0 4 8 76 80 0 0 0 0 -231 -232 null null null 0 0 0 37 335 .92 1 70 3700 6540 188 195 320 327 -50 63 259 -196 null 61 -198 null null null null
16 14445 7128 162 182 14283 6946 15160 7354 174 195 14998 7172 0 0 2454 908 73 67 100 100 100 100 21229 22170 2.056 .486 .478 .49 .48 .06 52 350 .49 1 80 3850 6540 188 196 335 343 0 10917 279 10638 .745 11263 10984 1.343 .732 -.425 -.449
17 1777 468 180 199 1597 269 1756 470 191 209 1576 271 0 0 99 30 78 63 100 100 100 100 1866 1847 5.937 .168 .172 .16 .17 .01 52 392 .28 .99 80 4010 6540 188 196 351 359 0 717 305 412 .258 720 415 3.876 .263 -1.955 -1.925
18 70 71 173 190 -103 -119 48 43 181 196 -125 -147 0 0 63 66 71 47 5 5 3 3 -222 -272 null null null .78 .76 .22 37 339 1 1 70 4160 6540 188 195 366 373 -50 109 291 -182 null 66 -225 null null null null
19 9832 5275 164 178 9668 5097 9867 5344 167 184 9703 5166 0 0 501 257 37 33 100 100 100 100 14765 14869 1.897 .527 .532 .52 .53 .02 52 334 .54 1 80 4310 6540 188 196 381 389 0 8079 273 7806 .807 8185 7912 1.238 .815 -.309 -.294
20 14184 22721 166 178 14018 22543 15641 25157 168 185 15475 24979 0 0 3706 6182 48 41 100 100 100 100 36561 40454 .622 1.608 1.614 1.6 1.61 .2 69 266 1.61 1 90 4460 6540 187 196 395 404 0 34798 273 34526 2.463 38529 38256 .406 2.472 1.3 1.306

Total number of rows: 44544

Table truncated, full table size 9341 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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