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Sample GSM466863 Query DataSets for GSM466863
Status Public on Nov 10, 2009
Title Ribosome density experiment: miR-124 12 hrs. (5-20-08)
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/2008-06/80379.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 2161 3819 97 80 2064 3739 2184 4047 102 83 2087 3967 0 0 325 680 28 15 100 100 100 100 5803 6054 .552 1.812 1.901 1.8 1.89 .2 52 411 1.79 1 80 1270 5550 89 97 77 85 0 5318 111 5207 2.523 5636 5525 .396 2.647 1.335 1.404
2 2139 3815 100 82 2039 3733 2314 4168 110 89 2214 4086 0 0 658 1092 57 38 97 100 97 100 5772 6300 .546 1.831 1.846 2.11 1.85 1.8 64 314 1.78 1 90 1410 5540 87 96 90 99 0 5313 114 5199 2.55 5804 5690 .392 2.57 1.35 1.362
3 16659 16482 99 82 16560 16400 18426 18050 107 89 18327 17968 0 0 4986 4491 56 39 98 100 98 100 32960 36295 1.01 .99 .98 1.39 1.02 2.31 60 317 .99 .99 80 1570 5540 88 96 107 115 0 22953 114 22839 1.379 25137 25023 .725 1.365 .464 .449
4 2075 3724 95 79 1980 3645 2299 4150 98 81 2204 4071 0 0 706 1193 24 14 98 100 97 100 5625 6275 .543 1.841 1.847 2.7 1.89 4.98 64 298 1.8 1 90 1720 5540 87 96 121 130 0 5186 110 5076 2.564 5779 5669 .39 2.572 1.358 1.363
5 7915 7831 96 80 7819 7751 8117 8100 100 92 8021 8020 0 0 667 823 30 77 100 100 100 100 15570 16041 1.009 .991 1 .98 1.02 .09 52 304 .99 1 80 1870 5540 88 96 137 145 0 10906 111 10794 1.381 11280 11169 .724 1.392 .465 .478
6 4110 26011 97 81 4013 25930 4461 29731 102 95 4364 29650 0 0 1290 8109 31 80 99 100 99 100 29943 34014 .155 6.462 6.794 7.3 7.14 4.42 69 282 6.41 .99 90 2020 5540 87 96 151 160 0 36224 113 36111 8.998 41404 41291 .111 9.462 3.17 3.242
7 655 641 98 83 557 558 692 675 117 95 594 592 0 0 131 103 129 100 98 100 96 98 1115 1186 .998 1.002 .997 1.01 1.01 .18 52 299 .98 .99 80 2170 5540 88 96 167 175 0 893 116 777 1.395 940 824 .717 1.388 .48 .473
8 17423 19826 95 81 17328 19745 19756 22176 111 92 19661 22095 0 0 5233 6555 123 97 97 100 97 99 37073 41756 .878 1.139 1.124 1.5 1.16 2.3 72 326 1.14 .99 90 2330 5530 86 95 182 191 0 27610 113 27497 1.587 30883 30770 .63 1.565 .666 .646
9 61 51 89 78 -28 -27 59 49 92 78 -30 -29 0 0 13 8 18 12 3 0 0 0 -55 -59 null null null 0 0 0 37 299 .84 .98 70 2480 5540 88 95 198 205 -50 71 109 -38 null 68 -40 null null null null
10 150 148 93 79 57 69 160 159 97 82 67 80 0 0 29 32 23 21 85 88 77 77 126 147 .826 1.211 1.194 1.3 1.14 .79 60 317 .99 .99 80 2610 5530 87 95 211 219 0 206 110 96 1.686 221 111 .593 1.663 .753 .734
11 5685 16733 92 80 5593 16653 5704 16967 98 86 5612 16887 0 0 470 1471 39 49 100 100 100 100 22246 22499 .336 2.977 3.009 2.97 3.03 .16 52 290 2.95 1 80 2780 5550 89 97 228 236 0 23303 111 23191 4.146 23629 23517 .241 4.191 2.052 2.067
12 733 472 92 80 641 392 755 485 95 81 663 405 0 0 98 54 20 13 100 100 100 100 1033 1068 1.635 .612 .611 .62 .62 .11 58 297 .64 1 80 2910 5530 87 95 241 249 0 657 111 546 .852 675 564 1.174 .851 -.232 -.233
13 14684 6479 90 79 14594 6400 14861 6703 94 80 14771 6624 0 0 924 697 20 12 100 100 100 100 20994 21395 2.28 .439 .448 .43 .45 .04 44 360 .44 1 70 3070 5530 87 94 257 264 0 9023 110 8913 .611 9335 9225 1.637 .625 -.711 -.679
14 1448 1047 91 78 1357 969 1505 1129 93 78 1414 1051 0 0 252 241 20 12 100 98 100 98 2326 2465 1.4 .714 .743 .7 .74 .1 58 341 .73 1 80 3230 5530 87 95 273 281 0 1458 109 1349 .994 1572 1464 1.006 1.035 -.008 .05
15 48 39 90 77 -42 -38 48 39 92 78 -42 -38 0 0 3 3 21 14 0 0 0 0 -80 -80 null null null 0 0 0 37 324 .79 1 70 3380 5540 88 95 288 295 -50 54 107 -53 null 54 -53 null null null null
16 15968 9474 93 80 15875 9394 16453 10325 96 81 16360 10245 0 0 2102 2042 23 14 100 100 100 100 25269 26605 1.69 .592 .626 .57 .62 .09 51 349 .6 1 80 3520 5520 86 94 302 310 0 13194 111 13082 .824 14379 14267 1.213 .872 -.279 -.197
17 629 167 90 77 539 90 695 178 92 78 605 101 0 0 180 41 21 13 94 88 94 88 629 706 5.989 .167 .167 .16 .17 .04 72 352 .27 .99 90 3690 5520 85 94 318 327 0 233 107 125 .233 248 141 4.3 .232 -2.104 -2.105
18 56 50 89 79 -33 -29 51 43 93 80 -38 -36 0 0 14 13 24 14 0 0 0 0 -62 -74 null null null 0 0 0 37 313 .86 .99 70 3830 5540 88 95 333 340 -50 70 110 -40 null 60 -50 null null null null
19 8845 6128 96 80 8749 6048 9225 6634 103 84 9129 6554 0 0 1757 1568 43 21 100 100 100 100 14797 15683 1.447 .691 .718 .66 .71 .11 60 302 .7 1 80 3990 5520 86 94 349 357 0 8534 111 8423 .963 9239 9127 1.039 1 -.055 0
20 10325 20186 89 76 10236 20110 12110 23654 91 76 12021 23578 0 0 3706 7499 26 12 99 100 99 100 30346 35599 .509 1.965 1.961 2.43 2.04 2.92 79 271 1.96 1 100 4130 5520 85 95 362 372 0 28112 106 28006 2.736 32941 32835 .365 2.731 1.452 1.45

Total number of rows: 44544

Table truncated, full table size 9058 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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