NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM280066 Query DataSets for GSM280066
Status Public on Apr 08, 2008
Title Ago2 Hek293 FLAG-Ago2 Expression (3)
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 = 24.25; Parameter Scan Time = 13:56:17; Parameter PMT Volts = 336; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58787; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.55; 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 = 24.25; Parameter Scan Time = 13:56:17; Parameter PMT Volts = 342; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58786; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.46; 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/2007-02/72489.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 24200 7050 141 126 24059 6924 26010 7233 142 126 25869 7107 0 0 18774 5527 22 15 100 100 100 100 30983 32976 3.475 .288 .275 .279 .288 1.804 32 176 .288 .99 60 1770 5230 326 332 149 155 0 11088 198 10890 .453 11376 11177 2.209 .432 -1.144 -1.211
2 25251 7840 140 128 25111 7712 20139 6449 141 128 19999 6321 0 0 21613 6633 18 14 100 100 100 100 32823 26320 3.256 .307 .316 .287 .31 1.908 32 176 .304 .99 60 1920 5230 326 332 164 170 0 12330 201 12129 .483 10143 9941 2.07 .497 -1.05 -1.008
3 14537 39931 139 127 14398 39804 17341 48012 140 127 17202 47885 0 43 10461 27340 15 14 100 100 100 100 54202 65087 .362 2.765 2.784 3.139 2.666 1.53 32 232 2.745 .98 70 2060 5230 325 332 177 184 -100 62801 200 62601 4.348 75510 75310 .23 4.378 2.12 2.13
4 24483 8046 136 127 24347 7919 18520 5422 139 129 18384 5295 0 0 22280 7445 15 19 100 100 100 100 32266 23679 3.075 .325 .288 .318 .334 1.728 32 176 .328 .99 60 2210 5230 326 332 193 199 0 12654 200 12454 .512 8527 8328 1.955 .453 -.967 -1.142
5 6518 12802 136 127 6382 12675 6660 12737 139 128 6524 12610 0 0 5137 10200 21 14 100 100 96 100 19057 19134 .504 1.986 1.933 1.863 1.971 1.682 32 176 2.002 .99 60 2360 5230 326 332 208 214 0 20134 200 19934 3.124 20032 19832 .32 3.04 1.643 1.604
6 31579 43106 144 132 31435 42974 40545 55294 148 133 40401 55162 0 0 14238 21772 22 15 100 100 100 100 74409 95563 .731 1.367 1.365 1.319 1.423 1.612 32 176 1.409 .99 60 2500 5230 326 332 222 228 0 67794 208 67587 2.15 86963 86755 .465 2.147 1.104 1.103
7 3883 3909 144 134 3739 3775 4349 4228 145 134 4205 4094 0 0 905 702 21 14 100 100 100 100 7514 8299 .99 1.01 .974 1.027 .98 1.142 12 104 .982 .99 50 2640 5220 325 330 236 241 0 6148 211 5937 1.588 6650 6439 .63 1.531 .667 .615
8 14630 39049 145 132 14485 38917 17251 54207 211 145 17106 54075 0 43 10749 28591 608 126 78 100 71 100 53402 71181 .372 2.687 3.161 3.394 2.638 1.85 32 232 2.708 .98 70 2790 5230 325 332 250 257 -100 61414 208 61206 4.225 85253 85046 .237 4.972 2.079 2.314
9 25008 8206 153 133 24855 8073 26672 9047 310 142 26519 8914 0 0 20256 6567 1125 63 81 90 75 81 32928 35433 3.079 .325 .336 .267 .33 1.928 32 176 .321 .99 60 2940 5220 325 331 266 272 0 12906 209 12697 .511 14229 14019 1.958 .529 -.969 -.92
10 9771 19052 150 139 9621 18913 10469 19425 163 143 10319 19286 0 0 2020 2279 42 26 100 100 100 100 28534 29605 .509 1.966 1.869 2.003 1.872 1.155 12 104 1.878 .98 50 3080 5220 325 330 280 285 0 29964 219 29745 3.092 30550 30332 .323 2.939 1.628 1.556
11 29480 47818 160 138 29320 47680 41279 64873 168 140 41119 64735 0 43 16416 24015 41 16 100 100 100 100 77000 105854 .615 1.626 1.574 1.883 1.576 1.631 32 176 1.584 .99 60 3220 5220 325 331 294 300 -100 75205 217 74988 2.558 102028 101811 .391 2.476 1.355 1.308
12 3540 3508 152 138 3388 3370 4267 4064 198 147 4115 3926 0 0 1462 1416 351 84 100 100 91 100 6758 8041 1.005 .995 .954 .991 .974 1.216 12 104 .989 .97 50 3370 5210 324 329 309 314 0 5517 217 5300 1.564 6392 6175 .639 1.501 .646 .585
13 467 329 157 145 310 184 465 329 706 201 308 184 0 0 24 28 4338 448 0 0 0 0 494 492 1.685 .594 .597 .589 .604 1.159 12 68 .595 .94 40 3520 5220 326 330 325 329 0 517 228 289 .933 517 289 1.071 .94 -.099 -.09
14 301 473 148 138 153 335 307 493 260 149 159 355 0 0 36 58 874 93 0 100 0 100 488 514 .457 2.19 2.233 2.22 2.138 1.218 12 104 1.994 .94 50 3660 5220 325 330 338 343 0 744 217 527 3.444 775 558 .29 3.511 1.784 1.812
15 27480 26662 152 144 27328 26518 29100 27079 158 146 28948 26935 0 0 4496 2577 28 17 100 100 100 100 53846 55883 1.031 .97 .93 .98 .937 1.135 12 104 .949 .98 50 3810 5210 324 329 353 358 0 41932 226 41706 1.526 42588 42362 .655 1.463 .61 .549
16 340 310 146 137 194 173 344 309 147 136 198 172 0 0 17 19 20 12 100 100 100 100 367 370 1.121 .892 .869 .89 .859 1.201 12 68 .908 .94 40 3960 5210 325 329 369 373 0 488 215 272 1.402 486 271 .713 1.366 .488 .45
17 168 147 140 135 28 12 175 146 142 135 35 11 0 0 19 15 16 11 75 41 58 33 40 46 2.333 .429 .314 .62 .476 2.49 12 104 .206 .18 50 4110 5200 323 328 383 388 -50 231 212 19 .674 230 17 1.484 .494 -.569 -1.017
18 349 136 141 135 208 1 346 136 143 135 205 1 0 0 20 12 25 12 100 16 100 0 209 206 208 .005 .005 .044 .062 2.163 12 68 -.011 -.08 40 4250 5210 325 329 398 402 0 214 212 2 .008 214 2 132.254 .008 -7.047 -7.026
19 3695 6804 141 142 3554 6662 5007 8794 142 141 4866 8652 0 0 2250 3789 14 14 100 100 100 100 10216 13518 .533 1.875 1.778 2.259 1.796 1.599 12 104 1.789 .98 50 4390 5200 323 328 411 416 0 10701 223 10478 2.948 13831 13607 .339 2.796 1.56 1.484
20 6211 7435 142 139 6069 7296 7620 8767 145 139 7478 8628 0 0 2540 2846 19 14 100 100 100 100 13365 16106 .832 1.202 1.154 1.226 1.178 1.222 12 104 1.203 .98 50 4540 5200 323 328 426 431 0 11693 219 11475 1.891 13788 13570 .529 1.815 .919 .86

Total number of rows: 49152

Table truncated, full table size 11111 Kbytes.




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