NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM466869 Query DataSets for GSM466869
Status Public on Nov 10, 2009
Title Ribosome density experiment: mock 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/2008-06/80377.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 2888 6395 172 89 2716 6306 3163 6870 195 94 2991 6781 0 0 678 1232 94 24 100 100 100 100 9022 9772 .431 2.322 2.267 2.39 2.33 .37 52 397 2.2 1 80 1630 5590 93 101 113 121 0 8618 120 8498 3.129 9258 9139 .32 3.055 1.646 1.611
2 2643 6035 168 88 2475 5947 3130 7048 183 96 2962 6960 0 0 824 1811 65 42 100 100 100 100 8422 9922 .416 2.403 2.35 2.46 2.38 .5 69 286 2.28 1 90 1770 5570 90 99 126 135 0 8133 119 8015 3.238 9498 9380 .309 3.167 1.695 1.663
3 18265 20092 164 93 18101 19999 22759 24344 176 98 22595 24251 0 0 6788 7218 54 36 100 100 99 100 38100 46846 .905 1.105 1.073 1.21 1.1 .62 79 270 1.1 1 100 1930 5580 91 101 142 152 0 27077 125 26952 1.489 32808 32682 .672 1.446 .574 .533
4 3028 6921 157 92 2871 6829 3327 7445 171 94 3170 7353 0 0 666 1360 55 20 100 100 100 100 9700 10523 .42 2.379 2.32 2.42 2.38 .34 61 272 2.29 1 90 2080 5580 91 100 157 166 0 9327 124 9203 3.206 10033 9909 .312 3.126 1.681 1.644
5 7964 9593 159 90 7805 9503 8644 10082 173 94 8485 9992 0 0 1417 1128 59 28 100 100 100 100 17308 18477 .821 1.218 1.178 1.23 1.19 .15 52 307 1.2 1 80 2230 5580 92 100 173 181 0 12928 121 12807 1.641 13587 13466 .609 1.587 .714 .666
6 5224 25737 165 93 5059 25644 6325 30931 180 100 6160 30838 0 0 1996 9375 66 39 100 100 98 100 30703 36998 .197 5.069 5.006 5.6 5.26 2.75 86 258 4.9 1 100 2380 5580 91 101 187 197 0 34685 125 34559 6.831 41685 41559 .146 6.747 2.772 2.754
7 787 669 163 94 624 575 843 710 190 104 680 616 0 0 132 109 87 46 100 100 100 100 1199 1296 1.085 .921 .906 .92 .92 .12 60 277 .84 1 80 2540 5580 92 100 204 212 0 902 127 775 1.242 957 830 .805 1.221 .312 .288
8 19308 21687 159 93 19149 21594 22889 24822 185 102 22730 24729 0 0 6016 6516 123 40 99 100 99 100 40743 47459 .887 1.128 1.088 1.27 1.14 .86 72 263 1.13 1 90 2700 5580 91 100 219 228 0 29227 125 29101 1.52 33452 33326 .658 1.466 .604 .552
9 60 49 149 84 -89 -35 60 49 163 87 -89 -35 0 0 5 3 105 19 0 0 0 0 -124 -124 null null null 0 0 0 37 277 .79 .99 70 2830 5590 93 100 233 240 -50 66 113 -47 null 66 -47 null null null null
10 161 128 149 83 12 45 163 137 155 87 14 54 0 0 23 27 39 27 9 74 1 51 57 68 .267 3.75 3.857 4.35 3.45 5.81 70 292 .78 .8 90 2990 5570 90 99 248 257 0 173 112 61 5.054 185 73 .198 5.198 2.337 2.378
11 6580 13379 149 87 6431 13292 7824 15455 177 95 7675 15368 0 0 2261 3648 134 41 100 100 100 100 19723 23043 .484 2.067 2.002 2.27 2 .91 64 302 2.02 1 90 3130 5580 91 100 262 271 0 18030 117 17913 2.785 20828 20711 .359 2.698 1.478 1.432
12 677 494 151 86 526 408 785 557 173 92 634 471 0 0 205 131 72 29 94 97 93 97 934 1105 1.289 .776 .743 .88 .75 .67 72 279 .73 .99 90 3300 5580 91 100 279 288 0 666 116 550 1.045 751 635 .957 1.001 .064 .002
13 16789 7157 151 84 16638 7073 19095 7949 164 86 18944 7865 0 0 4159 1791 67 13 100 100 100 100 23711 26809 2.352 .425 .415 .42 .42 .07 52 290 .43 .99 80 3440 5580 92 100 294 302 0 9645 113 9532 .573 10713 10599 1.745 .56 -.804 -.838
14 1671 1203 143 85 1528 1118 1852 1298 152 86 1709 1213 0 0 396 239 59 17 100 100 100 100 2646 2922 1.367 .732 .71 .75 .72 .16 64 330 .72 .99 90 3600 5580 91 100 309 318 0 1621 115 1507 .986 1749 1635 1.014 .957 -.02 -.064
15 73 52 142 87 -69 -35 54 43 148 88 -88 -44 0 0 37 20 40 18 3 3 0 0 -104 -132 null null null .49 .16 .58 37 315 .71 .99 70 3740 5590 93 100 324 331 -50 70 117 -47 null 58 -59 null null null null
16 15212 8459 147 86 15065 8373 16750 9073 153 88 16603 8987 0 0 3414 1620 39 14 100 100 100 100 23438 25590 1.799 .556 .541 .56 .55 .08 52 338 .56 1 80 3900 5590 93 101 340 348 0 11400 116 11284 .749 12227 12111 1.335 .729 -.417 -.455
17 2673 565 142 85 2531 480 2939 611 146 85 2797 526 0 0 622 126 34 14 100 100 100 100 3011 3323 5.273 .19 .188 .18 .19 .03 64 344 .21 1 90 4060 5580 91 100 355 364 0 761 115 647 .256 823 709 3.913 .253 -1.968 -1.98
18 94 57 133 83 -39 -26 59 46 140 83 -74 -37 0 0 57 24 37 14 11 3 3 3 -65 -111 null null null .28 .19 .18 37 261 .6 .95 70 4200 5600 94 101 370 377 -50 77 112 -35 null 62 -50 null null null null
19 9759 6431 149 91 9610 6340 11299 7228 165 92 11150 7137 0 0 2616 1457 65 19 100 100 100 100 15950 18287 1.516 .66 .64 .67 .65 .12 69 286 .66 1 90 4340 5570 90 99 383 392 0 8667 123 8544 .889 9741 9618 1.125 .863 -.17 -.213
20 10522 19750 186 108 10336 19642 13752 24271 431 192 13566 24163 0 0 4906 7656 747 238 95 100 90 100 29978 37729 .526 1.9 1.781 2.29 1.82 1.31 80 298 1.86 .99 100 4490 5580 91 101 398 408 0 26616 146 26471 2.561 32709 32564 .39 2.4 1.357 1.263

Total number of rows: 44544

Table truncated, full table size 9233 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap