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Sample GSM466868 Query DataSets for GSM466868
Status Public on Nov 10, 2009
Title Ribosome Occupancy experiment: mock 12 hrs. (5-14-08)
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/2008-06/80370.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
1 929 1011 171 195 758 816 974 1081 173 196 803 886 0 0 148 179 23 13 100 100 100 100 1574 1689 .929 1.077 1.103 1.06 1.1 .1 52 397 1.09 1 80 1530 6440 178 186 103 111 0 1242 240 1002 1.322 1328 1088 .756 1.355 .403 .439
2 1003 1105 177 200 826 905 1033 1167 177 200 856 967 0 0 144 158 26 14 100 100 100 100 1731 1823 .913 1.096 1.13 1.09 1.12 .13 52 293 1.1 .99 80 1680 6450 179 187 118 126 0 1357 246 1112 1.346 1433 1188 .743 1.388 .428 .473
3 12533 6631 177 204 12356 6427 15672 8147 179 203 15495 7943 0 0 4901 2333 24 14 100 100 100 100 18783 23438 1.923 .52 .513 .56 .52 .21 69 306 .53 .99 90 1830 6440 177 186 132 141 0 8145 251 7894 .639 10007 9756 1.565 .63 -.646 -.667
4 1062 1167 181 209 881 958 1059 1191 184 208 878 982 0 0 115 134 36 14 100 100 100 100 1839 1860 .92 1.087 1.118 1.08 1.11 .08 52 303 1.1 1 80 1990 6440 178 186 149 157 0 1433 257 1177 1.336 1463 1206 .749 1.374 .418 .458
5 1855 2047 182 213 1673 1834 1997 2223 186 214 1815 2010 0 0 369 369 40 13 100 100 100 100 3507 3825 .912 1.096 1.107 1.1 1.1 .11 52 295 1.1 1 80 2130 6440 178 186 163 171 0 2514 262 2253 1.346 2730 2469 .743 1.36 .429 .444
6 4586 8034 182 218 4404 7816 4991 9112 185 218 4809 8894 0 0 969 1885 23 13 100 100 100 100 12220 13703 .563 1.775 1.849 1.77 1.85 .22 80 238 1.75 .99 100 2290 6450 178 188 178 188 0 9868 268 9600 2.18 11192 10924 .459 2.272 1.124 1.184
7 351 285 183 220 168 65 356 285 188 222 173 65 0 0 31 17 34 17 100 100 100 96 233 238 2.585 .387 .376 .38 .38 .1 52 276 .82 .99 80 2430 6440 178 186 193 201 0 350 270 80 .475 350 80 2.104 .461 -1.073 -1.116
8 12168 6976 184 224 11984 6752 15735 9240 189 224 15551 9016 0 0 5838 3387 42 22 97 97 96 96 18736 24567 1.775 .563 .58 .58 .56 .21 69 289 .58 1 90 2590 6450 178 187 208 217 0 8569 275 8293 .692 11349 11074 1.445 .712 -.531 -.49
9 84 74 185 218 -101 -144 66 43 185 218 -119 -175 0 0 40 57 26 14 0 0 0 0 -245 -294 null null null 0 0 0 37 344 .87 1 70 2750 6440 178 185 225 232 -50 91 268 -177 null 53 -215 null null null null
10 109 100 190 223 -81 -123 96 80 192 222 -94 -143 0 0 37 44 38 13 3 0 0 0 -204 -237 null null null 0 0 0 37 331 .93 .99 70 2900 6440 178 185 240 247 -50 123 274 -151 null 98 -176 null null null null
11 2783 4245 185 223 2598 4022 2979 4539 187 222 2794 4316 0 0 504 687 23 15 100 100 100 100 6620 7110 .646 1.548 1.545 1.55 1.56 .13 52 313 1.51 1 80 3040 6440 178 186 254 262 0 5214 274 4940 1.902 5575 5301 .526 1.897 .927 .924
12 338 294 183 222 155 72 351 299 185 220 168 77 0 0 47 25 24 15 100 97 97 94 227 245 2.153 .465 .458 .46 .48 .15 69 291 .88 .99 90 3190 6440 177 186 268 277 0 361 273 88 .571 367 95 1.753 .563 -.81 -.829
13 2765 3517 188 222 2577 3295 2889 3689 189 222 2701 3467 0 0 525 734 27 14 100 100 100 100 5872 6168 .782 1.279 1.284 1.26 1.3 .15 52 320 1.28 1 80 3350 6430 177 185 285 293 0 4320 273 4047 1.571 4531 4258 .637 1.577 .651 .657
14 792 600 181 220 611 380 795 606 185 219 614 386 0 0 73 44 31 16 100 100 100 100 991 1000 1.608 .622 .629 .62 .63 .06 52 339 .77 1 80 3500 6440 178 186 300 308 0 737 270 467 .764 744 474 1.309 .772 -.389 -.373
15 64 50 172 213 -108 -163 62 40 174 212 -110 -173 0 0 14 28 23 15 0 0 0 0 -271 -283 null null null 0 0 0 37 336 .79 1 70 3650 6440 178 185 315 322 -50 61 262 -200 null 49 -212 null null null null
16 4160 5045 183 219 3977 4826 4296 5340 183 219 4113 5121 0 0 697 898 25 17 100 100 100 100 8803 9234 .824 1.213 1.245 1.2 1.23 .1 52 339 1.21 1 80 3800 6430 177 185 330 338 0 6197 269 5928 1.49 6559 6290 .671 1.529 .576 .613
17 913 545 189 221 724 324 929 545 187 217 740 324 0 0 92 37 30 29 100 100 100 100 1048 1064 2.235 .448 .438 .44 .45 .04 52 332 .61 1 80 3950 6440 178 186 345 353 0 669 271 398 .55 669 398 1.819 .538 -.863 -.895
18 165 164 190 220 -25 -56 184 211 183 207 -6 -9 0 0 79 84 42 48 11 0 8 0 -81 -15 null null null .53 .48 .44 37 277 .99 .91 70 4080 6470 181 188 358 365 -50 201 270 -69 null 259 -11 null null null null
19 2736 2771 194 225 2542 2546 3267 3308 190 218 3073 3083 0 0 1076 1044 36 39 97 100 97 99 5088 6156 .998 1.002 1.003 1.07 1.03 .39 69 312 1.01 1 90 4240 6420 175 184 373 382 0 3404 276 3127 1.23 4063 3787 .813 1.232 .299 .301
20 4401 8706 196 225 4205 8481 5462 10523 197 226 5266 10298 0 0 1849 3597 27 32 100 100 100 100 12686 15564 .496 2.017 1.956 2.06 2.04 .3 69 337 1.97 1 90 4390 6420 175 184 388 397 0 10693 276 10417 2.477 12925 12649 .404 2.402 1.309 1.264

Total number of rows: 44544

Table truncated, full table size 9239 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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