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Sample GSM280062 Query DataSets for GSM280062
Status Public on Apr 08, 2008
Title Ago2 Hek293 FLAG-Ago2 Expression (1)
Sample type RNA
 
Channel 1
Source name UNIVERSAL REFERENCE
Organism Homo sapiens
Characteristics UNIVERSAL REFERENCE
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name amplified RNA from HEK293T cells
Organism Homo sapiens
Characteristics amplified RNA from HEK293T cells
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 250, 1940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.69; Parameter Scan Time = 13:03:17; Parameter PMT Volts = 334; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58734; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.69; Parameter Scan Time = 13:03:17; Parameter PMT Volts = 333; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58733; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.47; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan
Description Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72487.gif
Measurement: mass(absolute) 10 ug
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 Apr 07, 2008
Last update date Apr 07, 2008
Contact name Daniel Hogan
Organization name Stanford University
Street address 279 Campus Dr B439
City Stanford
State/province CA
ZIP/Postal code 94025
Country USA
 
Platform ID GPL6697
Series (2)
GSE11080 Expression data HEK293T cells transfected with either Ago2, Ago2 + miR-1, Ago2 + miR-124, mock
GSE11082 Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance

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 15190 5402 142 126 15048 5276 14544 5571 144 126 14402 5445 0 0 11537 4132 15 13 100 96 100 93 20324 19847 2.852 .351 .378 .308 .35 1.908 32 176 .351 .99 60 2010 5190 322 328 173 179 0 7827 183 7644 .508 8071 7889 1.969 .548 -.977 -.868
2 17221 6099 142 126 17079 5973 20489 5983 143 126 20347 5857 0 0 13051 4673 14 12 100 100 100 100 23052 26204 2.859 .35 .288 .392 .361 1.475 32 176 .351 .99 60 2150 5190 322 328 187 193 0 8836 183 8654 .507 8668 8486 1.974 .417 -.981 -1.262
3 12292 38392 143 129 12149 38263 16019 54018 145 130 15876 53889 0 37 8398 28911 14 14 100 100 100 100 50412 69765 .318 3.149 3.394 2.715 3.257 1.542 32 231 3.329 .99 70 2310 5190 321 328 202 209 -100 55623 187 55437 4.563 78263 78076 .219 4.918 2.19 2.298
4 17189 6066 146 126 17043 5940 16559 5431 147 126 16413 5305 0 0 14798 5262 15 11 100 100 100 100 22983 21718 2.869 .349 .323 .319 .353 2.053 32 176 .349 .99 60 2450 5190 322 328 217 223 0 8789 183 8606 .505 7869 7686 1.98 .468 -.986 -1.095
5 5991 13615 145 127 5846 13488 7776 17349 146 127 7631 17222 0 0 4156 9643 14 13 96 100 93 100 19334 24853 .433 2.307 2.257 2.349 2.331 1.74 32 176 2.327 .99 60 2590 5180 321 327 231 237 0 19726 184 19542 3.343 25136 24952 .299 3.27 1.741 1.709
6 23852 25542 148 128 23704 25414 30734 30188 148 130 30586 30060 0 0 12668 12060 19 16 100 100 100 100 49118 60646 .933 1.072 .983 1.144 1.039 1.354 32 231 1.021 .99 70 2730 5180 320 327 244 251 0 37006 185 36821 1.553 43737 43552 .644 1.424 .635 .51
7 3095 3060 145 130 2950 2930 3308 3124 146 131 3163 2994 0 0 428 267 12 12 100 100 100 100 5880 6157 1.007 .993 .947 1 .983 1.095 12 104 .971 .99 50 2880 5180 321 326 260 265 0 4433 188 4245 1.439 4526 4338 .695 1.371 .525 .456
8 7701 24206 144 128 7557 24078 1931 8999 145 128 1787 8871 0 25 8673 28259 14 12 92 96 84 96 31635 10658 .314 3.186 4.964 3.11 3.258 1.711 52 302 3.263 .99 80 3040 5180 320 328 275 283 -100 35070 185 34885 4.616 13038 12853 .217 7.192 2.207 2.846
9 15971 5633 145 127 15826 5506 13570 5724 146 128 13425 5597 0 0 12080 4126 14 12 100 100 100 100 21332 19022 2.874 .348 .417 .293 .348 2.048 32 170 .342 .99 60 3180 5180 321 327 290 296 0 8161 184 7977 .504 8293 8109 1.984 .604 -.988 -.727
10 8558 20409 143 133 8415 20276 9708 22335 145 134 9565 22202 0 0 2425 4577 16 18 100 100 100 100 28691 31767 .415 2.41 2.321 2.473 2.326 1.161 12 104 2.347 .98 50 3320 5170 320 325 304 309 0 29569 193 29376 3.491 32360 32167 .286 3.363 1.804 1.75
11 31537 37940 142 129 31395 37811 36900 41827 143 129 36758 41698 0 0 10502 11205 13 11 100 100 100 100 69206 78456 .83 1.204 1.134 1.272 1.16 1.35 32 176 1.194 .98 60 3470 5180 321 327 319 325 0 54969 187 54782 1.745 60600 60413 .573 1.644 .803 .717
12 2980 2914 141 128 2839 2786 3158 3030 142 129 3017 2902 0 0 643 383 13 12 100 100 100 100 5625 5919 1.019 .981 .962 1.002 .953 1.15 12 104 .953 .99 50 3610 5180 321 326 333 338 0 4222 185 4036 1.422 4390 4205 .703 1.394 .508 .479
13 346 271 143 127 203 144 352 267 145 126 209 140 0 0 29 16 15 11 100 100 100 100 347 349 1.41 .709 .67 .712 .696 1.144 12 68 .678 .95 40 3760 5170 321 325 349 353 0 393 184 209 1.028 387 203 .973 .971 .039 -.043
14 247 323 138 127 109 196 245 330 139 127 107 203 0 0 17 21 12 9 100 100 100 100 305 310 .556 1.798 1.897 1.814 1.893 1.226 12 68 1.946 .91 40 3910 5170 321 325 364 368 0 468 184 284 2.605 478 294 .384 2.749 1.381 1.459
15 14497 16526 142 130 14355 16396 15859 15958 144 131 15717 15828 0 0 9775 11321 16 27 100 100 100 100 30751 31545 .876 1.142 1.007 .985 1.136 1.713 32 176 1.151 .98 60 4060 5170 320 326 378 384 0 23943 188 23755 1.655 23120 22932 .604 1.459 .727 .545
16 258 162 145 131 113 31 256 163 147 133 111 32 0 0 23 16 21 34 100 50 100 0 144 143 3.645 .274 .288 .236 .25 2.072 12 104 .307 .75 50 4210 5170 320 325 393 398 0 235 190 45 .397 236 46 2.516 .418 -1.331 -1.26
17 157 116 141 129 16 -13 162 115 142 128 21 -14 0 0 21 12 14 11 66 0 25 0 3 7 null null null .229 .462 6.544 12 104 .107 .08 50 4350 5160 319 324 407 412 -50 168 187 -19 null 167 -20 null null null null
18 253 124 144 129 109 -5 259 124 145 130 115 -5 0 0 26 12 14 11 100 8 100 8 104 110 null null null .038 .097 9.495 12 104 -.059 -.22 50 4490 5170 320 325 421 426 0 180 187 -7 null 180 -7 null null null null
19 4015 8174 144 134 3871 8040 4127 8321 144 134 3983 8187 0 0 361 656 13 12 100 100 100 100 11911 12170 .481 2.077 2.055 2.079 2.042 1.106 12 104 2.099 .99 50 4640 5160 319 324 436 441 0 11843 194 11649 3.009 12056 11862 .332 2.978 1.589 1.574
20 5628 7346 146 131 5482 7215 6311 8008 147 133 6165 7877 0 0 1557 1370 16 15 100 100 100 100 12697 14042 .76 1.316 1.278 1.364 1.278 1.186 12 104 1.239 .98 50 4780 5160 319 324 450 455 0 10643 190 10453 1.907 11602 11412 .524 1.851 .931 .888

Total number of rows: 49152

Table truncated, full table size 10974 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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