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Sample GSM466852 Query DataSets for GSM466852
Status Public on Nov 10, 2009
Title mock 12 hrs SS (5-14-08)
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 (5-14-08) (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/2008-07/80598.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 7875 17916 97 68 7778 17848 10430 21713 99 72 10333 21645 0 0 3705 7719 16 20 100 100 100 100 25626 31978 .436 2.295 2.095 2.372 2.176 1.47 80 443 2.282 .98 100 1530 7490 220 230 140 150 0 27433 104 27329 3.514 33247 33143 .285 3.207 1.813 1.681
2 10961 24814 101 70 10860 24744 11051 24078 103 79 10950 24008 0 0 585 2463 16 32 100 100 100 100 35604 34958 .439 2.278 2.193 2.272 2.237 1.095 52 258 2.386 .97 90 1690 7490 220 229 156 165 0 37995 107 37888 3.489 36868 36761 .287 3.357 1.803 1.747
3 8659 27387 100 70 8559 27317 10597 34216 102 77 10497 34146 0 0 3593 11260 18 28 100 100 100 100 35876 44643 .313 3.192 3.253 3.101 3.054 1.363 80 327 3.265 .98 100 1850 7490 220 230 172 182 0 41935 107 41828 4.887 52391 52284 .205 4.981 2.289 2.316
4 10896 25622 99 70 10797 25552 10995 24955 102 79 10896 24885 0 0 647 2564 22 29 100 100 100 100 36349 35781 .423 2.367 2.284 2.36 2.3 1.1 52 231 2.444 .98 90 2000 7490 220 229 187 196 0 39232 107 39125 3.624 38211 38104 .276 3.497 1.857 1.806
5 5286 12017 99 70 5187 11947 5534 12051 101 78 5435 11981 0 0 848 1195 15 25 100 100 100 100 17134 17416 .434 2.303 2.204 2.333 2.238 1.164 52 213 2.294 .98 90 2140 7490 220 229 201 210 0 18400 107 18293 3.527 18452 18345 .284 3.375 1.818 1.755
6 9739 28690 100 69 9639 28621 11953 36530 104 73 11853 36461 0 0 4115 12039 61 22 93 100 93 100 38260 48314 .337 2.969 3.076 4.081 2.984 4.333 120 418 3.044 .97 120 2290 7490 219 231 215 227 0 43930 106 43824 4.547 55934 55829 .22 4.71 2.185 2.236
7 873 1028 100 71 773 957 912 1054 113 84 812 983 0 0 135 160 95 63 100 100 100 100 1730 1795 .808 1.238 1.211 1.237 1.223 1.179 52 209 1.232 .95 80 2440 7490 221 229 232 240 0 1574 109 1465 1.896 1614 1505 .528 1.854 .923 .89
8 8533 29045 99 71 8434 28974 10523 35404 108 81 10424 35333 0 0 3598 11217 78 55 100 100 100 100 37408 45757 .291 3.435 3.39 3.348 3.312 1.392 80 300 3.422 .98 100 2600 7490 220 230 247 257 0 44473 109 44365 5.26 54210 54102 .19 5.19 2.395 2.376
9 497 159 99 69 398 90 530 152 99 71 431 83 0 0 102 38 11 10 100 100 100 94 488 514 4.422 .226 .193 .215 .217 1.484 52 205 .213 .88 80 2740 7480 220 228 262 270 0 243 106 138 .346 233 127 2.888 .295 -1.53 -1.762
10 286 169 98 71 188 98 291 166 99 73 193 95 0 0 51 27 13 12 100 100 100 100 286 288 1.918 .521 .492 .527 .519 1.302 52 234 .503 .92 80 2880 7480 220 228 276 284 0 259 109 150 .798 254 145 1.253 .754 -.325 -.408
11 8002 16062 100 72 7902 15990 8091 16402 101 76 7991 16330 0 0 777 1850 14 15 100 100 100 100 23892 24321 .494 2.024 2.044 2.019 2.027 1.06 52 278 2.111 .97 90 3040 7480 219 228 291 300 0 24594 110 24484 3.098 25115 25004 .323 3.129 1.632 1.646
12 740 860 98 71 642 789 738 878 99 74 640 807 0 0 75 113 12 16 100 100 100 100 1431 1447 .814 1.229 1.261 1.225 1.215 1.129 52 259 1.279 .96 90 3200 7480 219 228 307 316 0 1317 109 1208 1.882 1344 1236 .531 1.931 .912 .949
13 4484 9465 97 70 4387 9395 5106 10248 99 74 5009 10178 0 0 1413 2343 13 17 100 100 100 100 13782 15187 .467 2.142 2.032 2.208 2.063 1.226 52 243 2.104 .97 80 3340 7480 220 228 322 330 0 14493 107 14386 3.279 15692 15584 .305 3.111 1.713 1.638
14 2109 1182 97 69 2012 1113 2135 1196 98 72 2038 1127 0 0 173 118 12 13 100 100 100 100 3125 3165 1.808 .553 .553 .552 .546 1.11 52 307 .552 .98 90 3500 7480 219 228 337 346 0 1810 106 1704 .847 1831 1726 1.181 .847 -.24 -.24
15 86 58 99 71 -13 -13 86 54 100 74 -13 -17 0 0 11 15 13 12 0 1 0 1 -26 -30 null null null 1.24 1.063 1.837 52 291 1.31 .47 90 3650 7480 219 228 352 361 -50 89 109 -20 null 83 -26 null null null null
16 12713 14425 100 73 12613 14352 13363 15007 101 78 13263 14934 0 0 2111 2620 13 19 100 100 100 100 26965 28197 .879 1.138 1.126 1.133 1.138 1.079 52 255 1.15 .98 80 3800 7470 219 227 368 376 0 22087 112 21976 1.742 22979 22867 .574 1.724 .801 .786
17 2806 1280 100 72 2706 1208 2887 1311 100 76 2787 1239 0 0 371 197 13 25 100 100 100 100 3914 4026 2.24 .446 .445 .444 .441 1.102 52 307 .449 .98 90 3950 7470 218 227 382 391 0 1960 110 1850 .684 2007 1897 1.463 .681 -.549 -.555
18 85 57 98 70 -13 -13 83 55 100 73 -15 -15 0 0 11 9 15 14 0 1 0 0 -26 -30 null null null 1.089 1 2.535 52 261 1.025 .64 90 4110 7480 219 228 398 407 -50 87 107 -20 null 84 -23 null null null null
19 13981 8629 101 74 13880 8555 14677 8768 128 100 14576 8694 0 0 1956 879 150 131 100 100 100 100 22435 23270 1.622 .616 .596 .621 .605 1.117 52 284 .604 .98 90 4240 7470 218 227 411 420 0 13213 113 13099 .944 13425 13312 1.06 .913 -.084 -.131
20 15883 28785 102 77 15781 28708 16617 30716 121 97 16515 30639 0 0 2121 4487 108 115 100 100 100 100 44489 47154 .55 1.819 1.855 1.814 1.84 1.065 52 314 1.897 .98 90 4400 7460 217 226 427 436 0 44075 118 43957 2.785 47032 46914 .359 2.841 1.478 1.506

Total number of rows: 44544

Table truncated, full table size 9793 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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