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Sample GSM466864 Query DataSets for GSM466864
Status Public on Nov 10, 2009
Title Ribosome Occupancy experiment: mock 12 hrs. (5-12-08)
Sample type RNA
 
Channel 1
Source name aRNA generated from pooled mRNA unassociated with ribosomes
Organism Homo sapiens
Characteristics source1: pooled mRNA unassociated with ribosomes
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 at least one ribosome
Organism Homo sapiens
Characteristics source2: pooled mRNA associated with at least one ribosome
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/2008-06/80366.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 1272 1310 133 101 1139 1209 1380 1401 138 103 1247 1300 0 0 354 284 39 18 100 100 100 100 2348 2547 .942 1.061 1.043 1.21 1.05 .67 37 440 1.03 1 70 1430 6750 209 216 93 100 0 1589 123 1467 1.288 1699 1577 .777 1.265 .365 .339
2 1345 1419 134 104 1211 1315 1441 1492 138 105 1307 1388 0 0 273 196 29 18 100 100 100 100 2526 2695 .921 1.086 1.062 1.14 1.08 .4 52 330 1.05 1 80 1600 6760 210 218 110 118 0 1721 126 1595 1.317 1810 1684 .759 1.288 .397 .365
3 19021 13116 138 105 18883 13011 22016 14716 143 109 21878 14611 0 0 6518 3759 43 36 100 100 100 100 31894 36489 1.451 .689 .668 .77 .68 .36 52 308 .68 1 80 1750 6760 210 218 125 133 0 15910 127 15783 .836 17851 17724 1.196 .81 -.259 -.304
4 1356 1446 136 104 1220 1342 1466 1519 141 108 1330 1415 0 0 350 247 42 36 100 100 100 100 2562 2745 .909 1.1 1.064 1.23 1.08 .54 52 306 1.06 .99 80 1910 6760 210 218 141 149 0 1754 126 1628 1.334 1843 1716 .749 1.291 .416 .368
5 3518 4187 139 105 3379 4082 3514 4191 142 107 3375 4086 0 0 110 80 45 12 100 100 100 100 7461 7461 .828 1.208 1.211 1.2 1.22 .03 37 310 1.19 1 70 2050 6750 209 216 155 162 0 5079 127 4952 1.465 5084 4956 .682 1.469 .551 .554
6 7480 12186 141 109 7339 12077 8891 14273 146 113 8750 14164 0 0 2979 4462 48 60 100 100 99 100 19416 22914 .608 1.646 1.619 1.94 1.67 1.4 69 303 1.62 1 90 2200 6740 207 216 169 178 0 14782 132 14650 1.996 17314 17181 .501 1.964 .997 .973
7 493 364 140 107 353 257 510 372 147 113 370 265 0 0 77 36 53 61 100 100 98 98 610 635 1.374 .728 .716 .75 .73 .16 52 300 .74 .99 80 2360 6750 209 217 186 194 0 442 130 312 .883 451 321 1.132 .869 -.179 -.203
8 19906 13354 136 104 19770 13250 21811 13757 167 115 21675 13653 0 0 4758 1950 213 83 100 100 100 100 33020 35328 1.492 .67 .63 .73 .66 .35 52 301 .66 .99 80 2510 6760 210 218 201 209 0 16199 126 16073 .813 16688 16562 1.23 .764 -.299 -.388
9 69 52 131 103 -62 -51 67 51 142 107 -64 -52 0 0 12 8 122 58 0 0 0 0 -113 -116 null null null 0 0 0 37 346 .76 .99 70 2660 6750 209 216 216 223 -50 63 125 -62 null 62 -63 null null null null
10 114 114 131 101 -17 13 109 111 133 101 -22 10 0 0 19 14 25 12 5 38 0 14 -4 -12 null null null 2.65 1.96 1.51 37 344 .98 .22 70 2810 6750 209 216 231 238 -50 138 123 16 null 135 12 null null null null
11 3866 7198 129 100 3737 7098 4485 8129 129 101 4356 8029 0 0 1386 2299 21 13 100 100 96 100 10835 12385 .526 1.899 1.843 2.73 1.89 4.48 52 356 1.85 1 80 2960 6740 208 216 246 254 0 8731 121 8610 2.304 9861 9739 .434 2.236 1.204 1.161
12 472 389 129 100 343 289 482 403 130 100 353 303 0 0 60 49 21 11 100 100 100 100 632 656 1.187 .843 .858 .84 .85 .1 37 352 .83 1 70 3110 6740 208 215 261 268 0 472 121 351 1.022 489 368 .978 1.041 .031 .058
13 7579 6840 129 100 7450 6740 8331 7435 130 100 8202 7335 0 0 2124 1721 20 10 100 100 100 100 14190 15537 1.105 .905 .894 .97 .89 .37 37 366 .9 1 70 3260 6730 207 214 276 283 0 8297 121 8176 1.097 9019 8898 .911 1.085 .134 .117
14 1109 1115 129 100 980 1015 1155 1150 131 100 1026 1050 0 0 190 156 21 10 100 100 100 100 1995 2076 .966 1.036 1.023 1.06 1.03 .23 52 331 1.01 1 80 3420 6750 209 217 292 300 0 1353 121 1231 1.256 1395 1274 .796 1.241 .329 .312
15 65 44 126 98 -61 -54 54 39 128 98 -72 -59 0 0 32 16 21 10 5 3 3 0 -115 -131 null null null 1.81 1.82 0 37 327 .69 .99 70 3560 6750 209 216 306 313 -50 53 119 -66 null 47 -72 null null null null
16 8086 8279 126 98 7960 8181 8361 8476 128 97 8235 8378 0 0 1445 1049 27 11 100 100 100 100 16141 16613 .973 1.028 1.017 1.04 1.03 .17 52 337 1.03 1 80 3720 6740 208 216 322 330 0 10043 119 9924 1.247 10282 10163 .802 1.234 .318 .303
17 3068 905 126 98 2942 807 3255 944 129 98 3129 846 0 0 693 153 29 11 100 100 100 100 3749 3975 3.646 .274 .27 .28 .27 .09 52 345 .3 1 80 3870 6740 208 216 337 345 0 1098 119 979 .333 1145 1026 3.005 .328 -1.588 -1.608
18 76 53 126 98 -50 -45 61 42 128 99 -65 -56 0 0 32 26 25 13 3 5 0 0 -95 -121 null null null 4.07 .39 8.35 37 344 .7 .99 70 4010 6750 209 216 351 358 -50 64 119 -55 null 51 -68 null null null null
19 4275 5430 125 98 4150 5332 4299 5435 126 98 4174 5337 0 0 334 205 20 12 100 100 100 100 9482 9511 .778 1.285 1.279 1.28 1.28 .13 52 311 1.28 1 80 4180 6740 208 216 368 376 0 6587 119 6468 1.559 6593 6474 .642 1.551 .64 .633
20 9257 15635 122 95 9135 15540 11194 18045 122 94 11072 17950 0 0 3618 4531 22 13 100 100 100 100 24675 29022 .588 1.701 1.621 2.61 1.61 3.85 69 296 1.67 .99 90 4320 6730 206 215 381 390 0 18966 115 18851 2.064 21889 21774 .485 1.967 1.045 .976

Total number of rows: 44544

Table truncated, full table size 9115 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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