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Sample GSM466862 Query DataSets for GSM466862
Status Public on Nov 10, 2009
Title Ribosome Occupancy experiment: miR-124 12 hrs. (5-20-08)
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/2008-06/80380.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 1055 1226 73 63 982 1163 1097 1287 75 64 1024 1224 0 0 152 163 15 8 100 100 100 100 2145 2248 .844 1.184 1.195 1.2 1.19 .22 51 388 1.17 .99 80 1270 5560 90 98 77 85 0 1483 76 1407 1.432 1557 1480 .698 1.446 .518 .532
2 1102 1304 71 61 1031 1243 1181 1372 75 62 1110 1311 0 0 225 182 30 9 100 100 100 100 2274 2421 .829 1.206 1.181 1.27 1.2 .42 60 302 1.18 1 80 1420 5560 90 98 92 100 0 1577 74 1503 1.458 1659 1586 .686 1.428 .544 .514
3 27521 10370 73 62 27448 10308 30839 11291 114 73 30766 11229 0 0 8503 2792 352 118 98 100 97 100 37756 41995 2.663 .376 .365 1.29 .37 6.09 58 284 .38 1 80 1580 5560 90 98 108 116 0 12542 75 12467 .454 13656 13581 2.202 .441 -1.139 -1.18
4 1024 1237 72 61 952 1176 1192 1392 75 63 1120 1331 0 0 377 358 32 28 92 98 92 95 2128 2451 .81 1.235 1.188 2.06 1.2 4.09 60 304 1.2 .99 80 1720 5560 90 98 122 130 0 1496 74 1422 1.494 1684 1610 .669 1.437 .579 .523
5 2857 3323 78 65 2779 3258 2977 3422 85 68 2899 3357 0 0 439 353 36 24 100 100 100 100 6037 6256 .853 1.172 1.158 1.19 1.18 .2 52 330 1.16 1 80 1880 5550 89 97 138 146 0 4019 79 3940 1.418 4139 4060 .705 1.4 .504 .486
6 10377 14147 85 69 10292 14078 11841 15688 95 75 11756 15619 0 0 3163 3525 54 34 99 100 99 100 24370 27375 .731 1.368 1.329 1.65 1.35 1.47 70 278 1.36 1 90 2030 5550 88 97 152 161 0 17110 83 17026 1.654 18973 18890 .604 1.607 .726 .684
7 441 356 85 70 356 286 446 357 92 74 361 287 0 0 27 19 34 30 100 100 100 100 642 648 1.245 .803 .795 .8 .81 .07 44 272 .81 1 70 2180 5550 89 96 168 175 0 431 85 346 .972 432 347 1.029 .962 -.042 -.057
8 28676 10909 88 72 28588 10837 31022 11725 134 88 30934 11653 0 0 7440 2602 414 137 98 100 97 100 39425 42587 2.638 .379 .377 1.13 .38 5.47 64 330 .38 1 90 2340 5550 88 97 183 192 0 13194 87 13107 .458 14180 14093 2.181 .456 -1.125 -1.134
9 61 47 81 68 -20 -21 61 45 91 70 -20 -23 0 0 7 6 45 23 0 0 0 0 -41 -43 null null null 0 0 0 37 352 .77 .99 70 2500 5540 88 95 200 207 -50 57 82 -25 null 54 -28 null null null null
10 108 105 81 68 27 37 108 107 88 70 27 39 0 0 11 8 36 23 21 91 0 21 64 66 .73 1.37 1.444 2.42 1.43 5.26 34 362 .97 .99 60 2630 5550 90 96 214 220 0 127 82 45 1.657 129 47 .603 1.747 .729 .805
11 5278 7995 81 68 5197 7927 5254 7919 89 73 5173 7851 0 0 302 340 59 50 100 100 100 100 13124 13024 .656 1.525 1.518 1.52 1.54 .06 44 374 1.51 1 70 2790 5540 88 95 229 236 0 9669 82 9587 1.845 9577 9495 .542 1.836 .883 .876
12 537 436 80 67 457 369 557 447 85 69 477 380 0 0 87 48 26 19 100 100 100 100 826 857 1.238 .807 .797 .83 .81 .18 51 318 .81 1 80 2940 5550 89 97 244 252 0 527 81 446 .977 541 460 1.024 .963 -.034 -.054
13 4428 6203 81 67 4347 6136 4448 6246 86 69 4367 6179 0 0 317 413 29 14 100 100 100 100 10483 10546 .708 1.412 1.415 1.41 1.43 .1 44 329 1.42 1 70 3090 5550 89 96 259 266 0 7502 81 7421 1.707 7554 7473 .586 1.711 .772 .775
14 1085 835 83 69 1002 766 1141 876 90 73 1058 807 0 0 231 154 41 32 98 100 98 100 1768 1865 1.308 .764 .763 .86 .77 .74 60 360 .77 1 80 3240 5550 89 97 274 282 0 1010 83 926 .925 1059 976 1.082 .922 -.113 -.116
15 47 39 85 70 -38 -31 47 39 91 74 -38 -31 0 0 6 4 35 26 0 0 0 0 -69 -69 null null null 0 0 0 37 340 .83 1 70 3400 5540 88 95 290 297 -50 47 85 -37 null 47 -37 null null null null
16 8258 8264 86 71 8172 8193 8501 8542 93 74 8415 8471 0 0 1358 1364 41 18 100 100 100 100 16365 16886 .997 1.003 1.007 1.01 1.02 .14 52 327 1.01 1 80 3550 5550 89 97 305 313 0 9995 86 9909 1.213 10331 10245 .825 1.217 .278 .284
17 630 252 84 70 546 182 628 257 88 72 544 187 0 0 59 19 25 17 100 100 100 100 728 731 3 .333 .344 .33 .33 .03 51 337 .41 1 80 3690 5550 89 97 319 327 0 305 85 220 .403 311 226 2.481 .416 -1.311 -1.266
18 47 41 87 74 -40 -33 48 39 97 77 -39 -35 0 0 4 8 53 25 0 0 0 0 -73 -74 null null null 0 0 0 37 351 .86 .99 70 3850 5540 88 95 335 342 -50 50 89 -40 null 47 -42 null null null null
19 3766 4513 91 77 3675 4436 3881 4743 111 92 3790 4666 0 0 663 902 93 104 100 100 100 100 8111 8456 .828 1.207 1.231 1.18 1.25 .16 64 326 1.21 1 90 4010 5530 86 95 350 359 0 5458 93 5365 1.46 5736 5643 .685 1.489 .546 .574
20 11256 17261 88 74 11168 17187 12011 17891 107 100 11923 17817 0 0 2360 3028 156 233 100 100 100 100 28355 29740 .65 1.539 1.494 1.6 1.54 .48 60 273 1.53 1 80 4150 5550 89 97 365 373 0 20876 89 20786 1.861 21638 21548 .537 1.807 .896 .854

Total number of rows: 44544

Table truncated, full table size 9004 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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