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Sample GSM280060 Query DataSets for GSM280060
Status Public on Apr 08, 2008
Title Mock Hek293 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 = 24.44; Parameter Scan Time = 14:17:19; Parameter PMT Volts = 352; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58808; 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 = 24.44; Parameter Scan Time = 14:17:19; Parameter PMT Volts = 359; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58807; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.43; 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/2007-02/72492.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 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 24163 6881 172 158 23991 6723 29320 8833 195 169 29148 8675 0 0 11967 3422 235 101 100 100 100 100 30714 37823 3.568 .28 .298 .276 .283 1.113 12 104 .275 .99 50 2110 5230 326 331 183 188 0 9723 223 9500 .396 12482 12258 2.525 .421 -1.336 -1.25
2 19872 5506 175 157 19697 5349 21805 5000 174 159 21630 4843 0 0 16165 4672 21 23 100 93 100 84 25046 26473 3.682 .272 .224 .196 .273 2.174 32 176 .276 .98 60 2270 5230 326 332 199 205 0 7780 222 7559 .384 7065 6843 2.606 .316 -1.382 -1.66
3 22150 41799 181 163 21969 41636 25099 42003 180 166 24918 41840 0 37 14236 25124 19 21 100 100 100 100 63605 66758 .528 1.895 1.679 1.785 1.813 1.665 32 176 1.866 .98 60 2410 5230 326 332 213 219 -100 59065 230 58835 2.678 59353 59123 .373 2.373 1.421 1.247
4 21762 6205 179 165 21583 6040 14723 3597 180 166 14544 3432 0 0 18732 5555 20 17 100 100 100 100 27623 17976 3.573 .28 .236 .22 .278 1.858 32 176 .286 .99 60 2560 5230 326 332 228 234 0 8768 233 8535 .395 5083 4850 2.529 .333 -1.338 -1.584
5 8169 16134 181 167 7988 15967 9805 19050 183 168 9624 18883 0 0 5326 12020 20 18 100 100 100 100 23955 28507 .5 1.999 1.962 1.522 1.951 1.717 32 176 2.113 .99 60 2710 5230 326 332 243 249 0 22798 236 22562 2.825 26919 26683 .354 2.773 1.498 1.471
6 34921 31846 189 171 34732 31675 39201 36086 197 180 39012 35915 0 0 10904 12633 80 116 100 100 100 100 66407 74927 1.097 .912 .921 .85 .914 1.381 32 232 .952 .98 70 2850 5230 325 332 256 263 0 45001 242 44759 1.289 50992 50750 .776 1.301 .366 .38
7 2340 2175 192 171 2148 2004 3173 2909 193 172 2981 2738 0 0 1330 1401 24 20 96 90 93 90 4152 5719 1.072 .933 .918 .728 .944 2.038 32 176 .972 .99 60 3000 5230 326 332 272 278 0 3073 242 2832 1.318 4111 3869 .759 1.298 .399 .376
8 22720 42884 188 173 22532 42711 25911 55873 189 173 25723 55700 0 46 13603 25353 21 19 100 100 100 100 65243 81423 .528 1.896 2.165 2.145 1.824 1.567 32 176 1.899 .99 60 3140 5230 326 332 286 292 -100 60598 244 60354 2.679 78952 78708 .373 3.06 1.421 1.613
9 18487 5243 189 167 18298 5076 15109 4748 191 169 14920 4581 0 0 13521 3859 31 24 100 100 100 100 23374 19501 3.605 .277 .307 .277 .28 1.951 32 176 .278 .99 60 3290 5230 326 332 301 307 0 7409 236 7173 .392 6709 6473 2.551 .434 -1.351 -1.205
10 7352 15081 187 164 7165 14917 6967 14639 186 166 6780 14475 0 0 4897 10567 22 18 100 100 100 100 22082 21255 .48 2.082 2.135 2.031 2.124 1.931 32 176 2.13 .99 60 3440 5230 326 332 316 322 0 21311 232 21079 2.942 20686 20454 .34 3.017 1.557 1.593
11 38547 43369 189 164 38358 43205 47339 50733 196 174 47150 50569 0 0 17304 18007 54 64 100 100 100 100 81563 97719 .888 1.126 1.073 1.282 1.104 2.11 32 230 1.136 .98 70 3590 5230 325 332 330 337 0 61283 232 61052 1.592 71689 71458 .628 1.516 .671 .6
12 3507 3349 188 164 3319 3185 3897 3750 198 174 3709 3586 0 0 887 907 95 97 100 100 100 100 6504 7295 1.042 .96 .967 .954 .984 1.212 12 104 .966 .98 50 3720 5220 325 330 344 349 0 4732 232 4501 1.356 5299 5067 .737 1.366 .439 .45
13 365 302 184 166 181 136 381 299 184 164 197 133 0 0 38 31 22 21 100 100 100 100 317 330 1.331 .751 .675 .747 .77 1.346 12 104 .588 .73 50 3870 5220 325 330 359 364 0 427 235 192 1.062 423 188 .942 .954 .086 -.068
14 305 407 180 160 125 247 305 415 183 161 125 255 0 0 27 28 25 17 100 100 100 100 372 380 .506 1.976 2.04 2.007 1.963 1.309 12 68 1.918 .92 40 4020 5220 326 330 375 379 0 575 226 349 2.792 586 360 .358 2.883 1.481 1.527
15 24668 18760 183 162 24485 18598 30879 19102 190 168 30696 18940 0 0 15188 11992 72 61 100 100 100 100 43083 49636 1.317 .76 .617 .652 .781 2.14 32 176 .767 .98 60 4170 5220 325 331 389 395 0 26509 229 26280 1.073 26992 26764 .932 .872 .102 -.198
16 330 270 180 161 150 109 333 279 181 162 153 118 0 0 40 44 19 17 100 91 100 91 259 271 1.376 .727 .771 .761 .768 1.22 12 104 .742 .85 50 4310 5210 324 329 403 408 0 382 228 154 1.027 394 167 .974 1.09 .038 .124
17 197 167 183 164 14 3 203 178 187 165 20 14 0 0 25 30 22 22 50 25 8 0 17 34 4.667 .214 .7 .695 .739 2.951 12 104 .756 .35 50 4460 5210 324 329 418 423 -50 236 232 4 .303 252 20 3.303 .989 -1.724 -.016
18 314 163 181 161 133 2 326 166 184 163 145 5 0 0 37 20 21 23 100 8 100 0 135 150 66.5 .015 .034 .087 .095 2.387 12 68 -.051 -.12 40 4600 5210 325 329 433 437 0 230 228 3 .021 235 7 47.061 .049 -5.556 -4.359
19 4282 8356 185 161 4097 8195 4571 9013 248 185 4386 8852 0 0 757 1349 491 207 100 100 100 100 12292 13238 .5 2 2.018 2.012 2.002 1.143 12 104 1.988 .98 50 4750 5210 324 329 447 452 0 11808 228 11580 2.826 12736 12508 .354 2.852 1.499 1.512
20 4747 5717 180 158 4567 5559 4581 4571 180 158 4401 4413 0 0 3258 4304 20 17 100 100 96 100 10126 8814 .822 1.217 1.003 1.059 1.259 1.646 32 176 1.264 .99 60 4900 5210 324 330 462 468 0 8079 223 7855 1.72 6459 6236 .581 1.417 .782 .503

Total number of rows: 49152

Table truncated, full table size 11050 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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