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Sample GSM466871 Query DataSets for GSM466871
Status Public on Nov 10, 2009
Title Ribosome density experiment: miR-124 12 hrs. (5-14-08)
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/2008-06/80371.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 2802 3128 78 87 2724 3041 2971 3408 82 89 2893 3321 0 0 817 874 21 17 100 100 100 100 5765 6214 .896 1.116 1.148 1.15 1.16 .24 60 399 1.12 .99 80 1430 6800 214 222 93 101 0 4805 134 4671 1.715 5235 5101 .583 1.763 .778 .818
2 3041 3430 73 78 2968 3352 3273 3791 75 79 3200 3713 0 0 907 981 13 14 100 100 100 100 6320 6913 .885 1.129 1.16 1.22 1.15 .71 60 300 1.14 .99 80 1590 6790 213 221 109 117 0 5269 120 5149 1.735 5823 5703 .576 1.782 .795 .834
3 23318 21391 77 83 23241 21308 27456 24944 78 84 27379 24861 0 0 8508 8182 12 14 100 100 100 100 44549 52240 1.091 .917 .908 .91 .93 .24 69 286 .92 1 90 1740 6790 212 221 123 132 0 32857 127 32729 1.408 38314 38187 .71 1.395 .494 .48
4 3331 3670 79 85 3252 3585 3491 3950 82 86 3412 3865 0 0 623 820 18 14 100 100 100 100 6837 7277 .907 1.102 1.133 1.08 1.15 .16 60 298 1.12 1 80 1900 6790 213 221 140 148 0 5637 131 5507 1.693 6067 5937 .591 1.74 .76 .799
5 9281 5308 82 90 9199 5218 9597 5466 88 92 9515 5376 0 0 807 632 33 19 100 100 100 100 14417 14891 1.763 .567 .565 .56 .58 .05 52 310 .58 1 80 2040 6790 213 221 154 162 0 8153 138 8015 .871 8396 8258 1.148 .868 -.199 -.204
6 9336 38154 85 96 9251 38058 9655 42509 95 110 9570 42413 0 0 1436 11447 53 100 100 100 100 100 47309 51983 .243 4.114 4.432 4.01 4.55 .8 80 284 4.09 .99 100 2180 6800 213 223 167 177 0 58605 147 58458 6.319 65294 65147 .158 6.807 2.66 2.767
7 835 618 88 103 747 515 861 637 103 122 773 534 0 0 90 93 84 123 100 98 100 98 1262 1307 1.45 .689 .691 .67 .7 .09 52 336 .75 1 80 2350 6790 213 221 185 193 0 949 158 791 1.059 978 820 .944 1.061 .083 .086
8 25734 25929 90 108 25644 25821 27925 28797 103 120 27835 28689 0 0 7458 8036 82 92 100 100 100 100 51465 56524 .993 1.007 1.031 .99 1.03 .16 69 278 1.01 1 90 2500 6790 212 221 199 208 0 39827 166 39661 1.547 44233 44067 .647 1.583 .629 .663
9 66 62 86 104 -20 -42 65 58 91 107 -21 -46 0 0 9 15 36 25 0 0 0 0 -62 -67 null null null 0 0 0 37 330 .94 .99 70 2640 6780 212 219 214 221 -50 95 160 -65 null 89 -71 null null null null
10 190 179 85 102 105 77 199 184 92 105 114 82 0 0 38 25 41 27 92 97 80 85 182 196 1.364 .733 .719 .79 .72 .33 60 317 .96 .99 80 2790 6800 214 222 229 237 0 275 157 118 1.126 283 126 .888 1.105 .172 .144
11 10220 20395 88 108 10132 20287 10243 21196 97 113 10155 21088 0 0 2694 4423 39 28 100 100 100 100 30419 31243 .499 2.002 2.077 2.07 2.08 .37 60 329 2 1 80 2940 6790 213 221 244 252 0 31327 166 31161 3.076 32557 32391 .325 3.19 1.621 1.673
12 1095 560 90 112 1005 448 1094 561 107 120 1004 449 0 0 137 54 77 53 100 100 100 100 1453 1453 2.243 .446 .447 .44 .44 .06 60 293 .52 1 80 3100 6790 213 221 260 268 0 860 172 688 .685 862 690 1.46 .687 -.546 -.542
13 14729 5764 88 110 14641 5654 14764 5796 102 116 14676 5686 0 0 3445 920 63 37 100 100 100 100 20295 20362 2.589 .386 .387 .42 .38 .29 52 316 .39 1 80 3250 6790 213 221 275 283 0 8854 169 8685 .593 8903 8734 1.686 .595 -.753 -.749
14 2009 1442 87 109 1922 1333 2213 1627 97 115 2126 1518 0 0 599 457 44 43 100 100 100 100 3255 3644 1.442 .694 .714 .68 .71 .12 60 312 .73 1 80 3410 6790 213 221 291 299 0 2215 167 2048 1.065 2499 2332 .939 1.097 .091 .133
15 49 42 86 107 -37 -65 50 42 95 112 -36 -65 0 0 4 4 37 41 0 0 0 0 -102 -101 null null null 0 0 0 37 316 .82 .95 70 3550 6790 213 220 305 312 -50 65 164 -100 null 65 -100 null null null null
16 21996 10046 85 104 21911 9942 22062 10116 94 108 21977 10012 0 0 3067 1317 46 50 100 100 100 100 31853 31989 2.204 .454 .456 .45 .47 .04 52 334 .46 1 80 3710 6790 213 221 321 329 0 15431 160 15271 .697 15538 15379 1.435 .7 -.521 -.515
17 993 287 86 106 907 181 1085 305 99 110 999 199 0 0 311 67 62 51 100 91 99 84 1088 1198 5.011 .2 .199 .19 .2 .04 69 323 .29 1 90 3850 6780 211 220 334 343 0 441 163 278 .307 468 306 3.262 .306 -1.706 -1.709
18 53 44 87 109 -34 -65 51 43 98 111 -36 -66 0 0 8 6 51 28 0 0 0 0 -99 -102 null null null 0 0 0 37 323 .84 .99 70 4000 6790 213 220 350 357 -50 68 167 -100 null 66 -101 null null null null
19 13080 6318 90 116 12990 6202 13352 6522 105 123 13262 6406 0 0 1972 1188 63 61 100 100 100 100 19192 19668 2.094 .477 .483 .46 .49 .05 60 318 .49 1 80 4160 6780 212 220 366 374 0 9705 178 9526 .733 10018 9840 1.364 .742 -.447 -.431
20 24398 32001 89 113 24309 31888 25656 33675 105 120 25567 33562 0 0 5821 6228 94 55 100 100 100 100 56197 59129 .762 1.312 1.313 1.34 1.32 .18 60 287 1.3 1 80 4310 6780 212 220 381 389 0 49154 174 48980 2.015 51725 51552 .496 2.016 1.011 1.012

Total number of rows: 44544

Table truncated, full table size 9237 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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