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Sample GSM466860 Query DataSets for GSM466860
Status Public on Nov 10, 2009
Title mock 12 hrs SS (5-20-08)
Sample type RNA
 
Channel 1
Source name universal reference
Organism Homo sapiens
Characteristics reference: universal reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name mock 12 hrs SS (5-20-08) (aRNA)
Organism Homo sapiens
Characteristics cell line: HEK293T
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/2008-07/80600.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)
GSE18835 mRNA abundance in HEK293T cells mock or miR-124 transfected
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 14489 18481 93 71 14396 18410 15849 17178 93 72 15756 17107 0 0 5246 8474 11 9 100 100 100 100 32806 32863 .782 1.279 1.086 1.297 1.306 1.819 52 359 1.356 .84 90 1550 7220 193 202 142 151 0 29980 115 29864 2.074 27866 27751 .482 1.761 1.053 .817
2 18261 17497 94 72 18167 17425 19478 16971 95 74 19384 16899 0 0 4654 6224 12 10 100 100 100 100 35592 36283 1.043 .959 .872 .949 .923 1.573 52 291 .98 .9 90 1710 7210 192 201 158 167 0 28383 117 28267 1.556 27530 27413 .643 1.414 .638 .5
3 14126 45577 97 78 14029 45499 16097 51535 106 89 16000 51457 0 0 5848 13056 38 46 98 100 98 100 59528 67457 .308 3.243 3.216 3.974 3.324 2.045 52 288 3.13 .97 90 1860 7210 192 201 173 182 0 73934 127 73808 5.261 83599 83473 .19 5.217 2.395 2.383
4 16007 19260 103 83 15904 19177 17318 17854 114 100 17215 17771 0 0 5037 8621 42 50 100 100 100 100 35081 34986 .829 1.206 1.032 1.194 1.147 1.987 52 287 1.327 .8 90 2010 7210 192 201 188 197 0 31243 135 31109 1.956 28962 28828 .511 1.675 .968 .744
5 5750 13599 101 84 5649 13515 6046 14248 106 88 5945 14164 0 0 1106 1684 22 21 100 100 100 100 19164 20109 .418 2.392 2.383 2.445 2.341 1.179 52 226 2.354 .99 80 2160 7210 193 201 204 212 0 22060 136 21924 3.881 23113 22977 .258 3.865 1.956 1.95
6 13090 40424 102 88 12988 40336 13659 46244 111 107 13557 46156 0 0 2868 11307 45 128 100 100 100 100 53324 59713 .322 3.106 3.405 3.052 3.221 1.237 80 402 3.153 .95 110 2310 7200 190 201 217 228 0 65575 143 65432 5.038 75016 74874 .198 5.523 2.333 2.465
7 937 1212 113 99 824 1113 968 1277 121 119 855 1178 0 0 197 207 48 129 100 100 100 100 1937 2033 .74 1.351 1.378 1.376 1.362 1.202 52 243 1.319 .99 80 2470 7200 192 200 235 243 0 1966 161 1805 2.191 2072 1911 .456 2.235 1.132 1.16
8 8677 36144 102 90 8575 36054 10667 45532 109 102 10565 45442 0 0 3953 16017 30 42 100 100 100 100 44629 56007 .238 4.205 4.301 4.023 4.086 1.316 80 336 4.241 .99 100 2620 7200 191 201 249 259 0 58632 146 58486 6.821 73861 73715 .147 6.977 2.77 2.803
9 629 178 101 90 528 88 669 178 107 93 568 88 0 0 114 27 22 21 100 100 100 94 616 656 6 .167 .155 .163 .16 1.367 52 233 .161 .9 80 2770 7200 192 200 265 273 0 289 146 143 .27 289 143 3.699 .251 -1.887 -1.992
10 316 231 99 83 217 148 332 230 104 89 233 147 0 0 63 38 20 21 100 100 98 98 365 380 1.466 .682 .631 .702 .677 1.375 52 243 .657 .94 80 2910 7200 192 200 279 287 0 375 135 240 1.106 373 238 .904 1.023 .146 .033
11 8030 20403 99 82 7931 20321 8952 21120 104 86 8853 21038 0 0 2407 4278 34 22 100 100 100 100 28252 29891 .39 2.562 2.376 2.75 2.432 1.365 52 301 2.473 .98 90 3060 7200 191 200 293 302 0 33097 133 32964 4.156 34261 34128 .241 3.855 2.055 1.947
12 795 931 97 78 698 853 795 955 103 84 698 877 0 0 85 115 39 33 100 100 100 100 1551 1575 .818 1.222 1.256 1.22 1.21 1.116 52 291 1.226 .99 90 3220 7200 191 200 309 318 0 1510 127 1384 1.982 1549 1423 .504 2.038 .987 1.027
13 4245 9273 96 76 4149 9197 4420 9538 100 80 4324 9462 0 0 1064 1833 23 29 100 100 100 100 13346 13786 .451 2.217 2.188 2.276 2.165 1.196 52 265 2.186 .99 80 3370 7190 191 199 325 333 0 15043 123 14919 3.596 15472 15349 .278 3.55 1.846 1.828
14 2188 1299 95 74 2093 1225 2275 1348 96 76 2180 1274 0 0 291 199 11 12 100 100 100 100 3318 3454 1.709 .585 .584 .583 .591 1.101 52 261 .586 .99 80 3520 7200 192 200 340 348 0 2107 120 1987 .949 2187 2067 1.053 .948 -.075 -.077
15 86 59 94 73 -8 -14 86 56 95 75 -8 -17 0 0 9 12 11 11 1 5 0 0 -22 -25 null null null 2.008 1.8 1.946 52 280 1.511 .31 90 3680 7200 191 200 355 364 -50 96 118 -23 null 91 -28 null null null null
16 11405 13294 95 73 11310 13221 12295 14112 95 75 12200 14039 0 0 2163 2867 12 11 100 100 100 100 24531 26239 .855 1.169 1.151 1.159 1.16 1.14 52 238 1.178 .99 80 3820 7190 191 199 370 378 0 21565 118 21447 1.896 22892 22774 .527 1.867 .923 .9
17 3067 1238 96 74 2971 1164 3191 1286 98 76 3095 1212 0 0 451 216 18 12 100 100 100 100 4135 4307 2.552 .392 .392 .389 .396 1.099 52 262 .391 .99 80 3970 7190 191 199 385 393 0 2008 120 1888 .636 2086 1966 1.573 .635 -.654 -.655
18 79 55 95 75 -16 -20 79 55 96 76 -16 -20 0 0 9 8 13 10 0 0 0 0 -36 -36 null null null 1.264 1.25 2.084 52 278 .843 .56 90 4130 7200 191 200 400 409 -50 89 122 -32 null 89 -32 null null null null
19 14498 9868 97 77 14401 9791 14727 10032 110 87 14630 9955 0 0 1267 1083 59 50 100 100 100 100 24192 24585 1.471 .68 .68 .678 .679 1.076 52 286 .67 .99 90 4270 7190 190 199 414 423 0 16008 125 15883 1.103 16274 16149 .907 1.104 .141 .143
20 15641 27966 99 78 15542 27888 17165 29784 113 91 17066 29706 0 0 3448 4843 67 57 100 100 100 100 43430 46772 .557 1.794 1.741 1.827 1.753 1.147 52 310 1.762 .99 90 4420 7180 189 198 429 438 0 45366 127 45239 2.911 48315 48189 .344 2.824 1.541 1.498

Total number of rows: 44544

Table truncated, full table size 9688 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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