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Sample GSM280063 Query DataSets for GSM280063
Status Public on Apr 08, 2008
Title Ago2 Hek293 FLAG-Ago2 Expression (2)
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 = 24.00; Parameter Scan Time = 13:29:42; Parameter PMT Volts = 360; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58761; 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 = 24.00; Parameter Scan Time = 13:29:42; Parameter PMT Volts = 358; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58760; 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/2007-02/72488.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 39831 13052 212 296 39619 12756 47491 15510 213 298 47279 15214 0 0 19219 5311 33 32 100 100 100 100 52375 62493 3.106 .322 .322 .353 .314 1.271 12 104 .302 .99 50 2160 5050 308 313 188 193 0 19735 448 19288 .487 23452 23005 2.054 .487 -1.038 -1.039
2 49662 16459 202 294 49460 16165 59004 19098 207 294 58802 18804 0 0 19529 5663 25 32 100 100 100 100 65625 77606 3.06 .327 .32 .339 .323 1.14 12 104 .312 .99 50 2310 5050 308 313 203 208 0 24887 445 24443 .494 28877 28433 2.024 .484 -1.017 -1.048
3 37967 65384 203 296 37764 65088 40385 65535 211 305 40182 65239 0 91 5221 522 36 38 100 100 100 100 102852 105421 .58 1.724 1.624 1.741 1.624 1.161 12 104 1.753 .98 50 2460 5050 308 313 218 223 -100 98865 448 98417 2.606 99093 98646 .384 2.455 1.382 1.296
4 27746 9058 202 287 27544 8771 20834 7887 205 288 20632 7600 3 0 25571 8181 26 23 100 100 100 96 36315 28232 3.14 .318 .368 .318 .332 1.986 32 176 .317 .99 60 2610 5050 308 314 233 239 0 13696 434 13262 .481 11926 11492 2.077 .557 -1.054 -.844
5 15637 29805 212 295 15425 29510 19952 37251 213 302 19740 36956 0 0 7869 14030 30 40 100 100 100 100 44935 56696 .523 1.913 1.872 2.006 1.89 1.243 12 104 1.899 .99 50 2750 5040 307 312 247 252 0 45067 446 44621 2.893 56326 55880 .346 2.831 1.532 1.501
6 34159 53791 216 313 33943 53478 36935 60161 283 569 36719 59848 0 16 9278 17860 500 1975 100 100 100 100 87421 96567 .635 1.576 1.63 1.46 1.6 1.325 12 104 1.617 .99 50 2900 5040 307 312 262 267 -100 81336 473 80862 2.382 90967 90494 .42 2.465 1.252 1.301
7 5317 6746 202 304 5115 6442 5845 7203 205 305 5643 6899 0 0 1208 1656 23 31 100 100 100 100 11557 12542 .794 1.259 1.223 1.25 1.299 1.148 12 104 1.263 .99 50 3040 5040 307 312 276 281 0 10200 460 9741 1.904 10891 10432 .525 1.849 .929 .886
8 38258 65062 211 300 38047 64762 40460 65535 215 314 40249 65235 0 83 4557 1204 29 56 100 100 100 100 102809 105484 .587 1.702 1.621 1.715 1.621 1.132 12 104 1.693 .98 50 3190 5040 307 312 291 296 -100 98378 454 97924 2.574 99093 98640 .389 2.451 1.364 1.293
9 47925 15645 204 297 47721 15348 56337 17825 215 301 56133 17528 0 0 15869 4235 65 72 100 100 100 100 63069 73661 3.109 .322 .312 .332 .318 1.134 12 104 .302 .99 50 3330 5040 307 312 305 310 0 23656 449 23207 .486 26953 26504 2.056 .472 -1.04 -1.083
10 17541 33244 209 299 17332 32945 18852 34547 208 301 18643 34248 0 0 3190 3684 27 31 100 100 100 100 50277 52891 .526 1.901 1.837 1.925 1.838 1.115 12 104 1.852 .98 50 3480 5040 307 312 320 325 0 50267 452 49815 2.874 52237 51785 .348 2.778 1.523 1.474
11 37553 54877 212 310 37341 54567 43590 65535 343 867 43378 65225 0 75 14613 20707 862 3777 100 91 100 91 91908 108603 .684 1.461 1.504 1.419 1.451 1.268 12 104 1.491 .98 50 3630 5030 306 311 335 340 -100 82978 469 82509 2.21 99093 98625 .453 2.274 1.144 1.185
12 5697 7277 206 299 5491 6978 5744 7243 209 301 5538 6944 0 0 358 437 30 28 100 100 100 100 12469 12482 .787 1.271 1.254 1.271 1.267 1.034 12 104 1.245 .99 50 3770 5040 307 312 349 354 0 11003 452 10551 1.922 10952 10500 .52 1.896 .942 .923
13 519 424 206 297 313 127 520 430 210 301 314 133 0 0 38 33 44 36 100 100 100 91 440 447 2.465 .406 .424 .392 .448 1.413 12 68 .417 .88 40 3920 5040 308 312 365 369 0 641 449 192 .614 650 201 1.63 .64 -.705 -.643
14 353 635 203 298 150 337 357 641 209 298 154 343 0 0 45 64 45 49 100 100 91 100 487 497 .445 2.247 2.227 2.326 2.433 1.325 12 68 2.312 .9 40 4060 5040 308 312 379 383 0 960 451 510 3.397 969 519 .294 3.368 1.764 1.752
15 39144 35761 208 296 38936 35465 41195 36665 211 298 40987 36369 0 0 4881 3029 29 25 100 100 100 100 74401 77356 1.098 .911 .887 .915 .897 1.088 12 104 .897 .98 50 4210 5030 306 311 393 398 0 54073 448 53625 1.377 55440 54992 .726 1.342 .462 .424
16 421 534 207 296 214 238 426 529 209 297 219 233 0 0 23 37 26 28 100 100 100 100 452 452 .899 1.112 1.064 1.104 1.16 1.206 12 68 .59 .78 40 4360 5030 307 311 409 413 0 807 448 360 1.682 800 352 .595 1.609 .75 .686
17 229 242 205 296 24 -54 230 225 207 300 25 -71 0 0 28 49 27 41 50 0 16 0 -30 -46 null null null .556 .556 1 12 104 11.69 .12 50 4510 5020 305 310 423 428 -50 366 448 -82 null 340 -107 null null null null
18 370 209 207 308 163 -99 409 187 208 307 202 -121 0 0 79 53 22 28 100 0 83 0 64 81 null null null .145 .145 1 12 104 -.728 -.83 50 4650 5020 305 310 437 442 -50 316 466 -150 null 283 -183 null null null null
19 5367 8661 214 306 5153 8355 6243 9732 216 309 6029 9426 0 0 1927 2019 29 30 100 100 100 100 13508 15455 .617 1.621 1.563 1.746 1.558 1.339 12 104 1.496 .98 50 4790 5030 306 311 451 456 0 13096 463 12633 2.452 14715 14253 .408 2.364 1.294 1.241
20 8570 9937 212 302 8358 9635 10057 11338 213 305 9845 11036 0 0 3113 2933 23 29 100 100 100 100 17993 20881 .867 1.153 1.121 1.206 1.111 1.227 12 104 1.116 .98 50 4940 5020 305 310 466 471 0 15025 457 14569 1.743 17144 16687 .574 1.695 .802 .761

Total number of rows: 49152

Table truncated, full table size 11150 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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