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Sample GSM466870 Query DataSets for GSM466870
Status Public on Nov 10, 2009
Title Ribosome Occupancy experiment: mock 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/2008-06/80378.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 1858 1663 87 76 1771 1587 1975 1740 90 77 1888 1664 0 0 405 246 17 12 100 100 100 100 3358 3552 1.116 .896 .881 .95 .89 .36 52 393 .89 1 80 1580 5600 94 102 108 116 0 2326 106 2219 1.253 2433 2327 .798 1.233 .326 .302
2 1796 1692 90 80 1706 1612 1986 1839 91 81 1896 1759 0 0 561 423 19 14 97 100 97 100 3318 3655 1.058 .945 .928 1.33 .93 2.27 64 308 .94 1 90 1730 5590 92 101 122 131 0 2366 112 2254 1.321 2572 2460 .757 1.297 .402 .376
3 35584 26055 92 88 35492 25967 39168 28053 131 105 39076 27965 0 0 8330 5284 542 240 100 100 100 100 61459 67041 1.367 .732 .716 .75 .72 .21 60 300 .73 1 80 1880 5590 93 101 138 146 0 36439 123 36316 1.023 39233 39110 .977 1.001 .033 .001
4 1846 1775 93 86 1753 1689 2047 1918 127 100 1954 1832 0 0 512 378 525 233 94 100 88 98 3442 3786 1.038 .963 .938 1.25 .96 1.74 64 319 .96 1 90 2030 5590 92 101 152 161 0 2482 120 2362 1.347 2682 2562 .742 1.311 .43 .391
5 3658 3601 93 85 3565 3516 3913 3770 95 84 3820 3685 0 0 666 486 25 13 100 100 100 100 7081 7505 1.014 .986 .965 1 .98 .19 52 325 .99 1 80 2190 5590 93 101 169 177 0 5036 119 4917 1.379 5272 5154 .725 1.349 .464 .432
6 18748 17058 95 86 18653 16972 19864 17824 96 87 19769 17738 0 0 3514 2493 18 14 100 100 100 100 35625 37507 1.099 .91 .897 .93 .9 .22 64 281 .91 1 90 2340 5590 92 101 183 192 0 23856 120 23736 1.273 24928 24807 .786 1.255 .348 .328
7 408 294 95 86 313 208 410 301 97 86 315 215 0 0 46 38 17 15 100 100 100 100 521 530 1.505 .665 .683 .66 .69 .09 52 314 .73 .99 80 2490 5580 92 100 199 207 0 411 120 291 .929 421 301 1.076 .955 -.106 -.067
8 35505 28478 94 87 35411 28391 39841 31275 108 90 39747 31188 0 0 9756 6422 130 43 100 100 100 100 63802 70935 1.247 .802 .785 1.05 .8 1.63 64 287 .8 1 90 2640 5590 92 101 213 222 0 39828 122 39706 1.121 43739 43618 .892 1.097 .165 .134
9 64 47 95 87 -31 -40 63 45 106 90 -32 -42 0 0 6 5 115 38 0 0 0 0 -71 -74 null null null 0 0 0 37 370 .71 .98 70 2790 5580 92 99 229 236 -50 66 122 -56 null 63 -59 null null null null
10 93 87 95 86 -2 1 95 88 97 87 0 2 0 0 9 9 19 13 0 11 0 0 -1 2 null null null 1.29 .75 1.36 37 366 .91 .14 70 2940 5580 92 99 244 251 -50 122 120 1 null 123 3 null null null null
11 4040 4787 98 90 3942 4697 4500 5321 101 90 4402 5231 0 0 1029 1115 31 13 100 100 100 100 8639 9633 .839 1.192 1.188 1.24 1.2 .34 60 340 1.19 1 80 3090 5580 92 100 259 267 0 6695 126 6569 1.666 7442 7316 .6 1.662 .737 .733
12 443 319 101 91 342 228 473 329 103 92 372 238 0 0 78 45 33 13 100 100 100 100 570 610 1.5 .667 .64 .68 .67 .16 60 318 .72 1 80 3250 5580 92 100 275 283 0 446 127 319 .932 460 333 1.073 .895 -.101 -.16
13 4810 5212 101 94 4709 5118 4870 5314 104 96 4769 5220 0 0 361 567 20 18 100 100 100 100 9827 9989 .92 1.087 1.095 1.08 1.1 .07 44 346 1.1 1 70 3400 5580 92 99 290 297 0 7289 131 7158 1.52 7432 7300 .658 1.531 .604 .614
14 801 609 103 96 698 513 828 613 105 98 725 517 0 0 110 52 23 20 100 100 100 100 1211 1242 1.361 .735 .713 .74 .72 .12 52 329 .76 1 80 3550 5590 93 101 305 313 0 852 134 717 1.028 857 723 .973 .997 .04 -.004
15 54 39 102 95 -48 -56 54 39 104 97 -48 -56 0 0 8 5 24 20 0 0 0 0 -104 -104 null null null 0 0 0 37 363 .72 1 70 3690 5580 92 99 319 326 -50 55 133 -78 null 55 -78 null null null null
16 9272 8078 101 95 9171 7983 10184 8479 103 97 10083 8384 0 0 2346 1325 20 20 100 100 100 100 17154 18467 1.149 .87 .831 .95 .85 .43 52 361 .87 1 80 3850 5580 92 100 335 343 0 11297 133 11165 1.217 11858 11725 .821 1.163 .284 .218
17 801 491 102 94 699 397 855 516 104 97 753 422 0 0 173 90 20 21 100 100 98 100 1096 1175 1.761 .568 .56 .61 .57 .33 58 313 .62 .99 80 4000 5590 93 101 350 358 0 687 131 555 .794 722 590 1.259 .784 -.332 -.351
18 56 41 104 96 -48 -55 52 39 105 97 -52 -57 0 0 13 8 20 16 0 0 0 0 -103 -109 null null null 0 0 0 37 341 .75 .99 70 4140 5580 92 99 364 371 -50 57 134 -77 null 55 -80 null null null null
19 3321 3539 104 95 3217 3444 4023 4000 107 98 3919 3905 0 0 1368 969 25 28 100 100 99 100 6661 7824 .934 1.071 .996 2.06 1.01 3.28 69 323 1.05 .99 90 4300 5580 91 100 379 388 0 4949 133 4817 1.497 5594 5461 .668 1.394 .582 .479
20 19084 18763 105 97 18979 18666 19384 19129 108 101 19279 19032 0 0 1370 1893 26 32 100 100 100 100 37645 38311 1.017 .984 .987 .97 1 .05 52 293 1.01 1 80 4460 5580 92 100 396 404 0 26241 136 26105 1.375 26753 26617 .727 1.381 .46 .465

Total number of rows: 44544

Table truncated, full table size 9129 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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