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Sample GSM280045 Query DataSets for GSM280045
Status Public on Apr 08, 2008
Title Ago2 Hek293 FLAG-Ago2 IP (8)
Sample type RNA
 
Channel 1
Source name amplified RNA from HEK293T cell lysate
Organism Homo sapiens
Characteristics amplified RNA from HEK293T cell lysate
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name amplified RNA after FLAG-Ago2 affinity purification
Organism Homo sapiens
Characteristics amplified RNA after FLAG-Ago2 affinity purification
Measurement: mass(absolute) 10 ug
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 = 680, 4880; 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 = 38.36; Parameter Scan Time = 16:58:23; Parameter PMT Volts = 580; Parameter Scan Date = 2007-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 337889; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; 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 = 38.36; Parameter Scan Time = 16:58:23; Parameter PMT Volts = 480; Parameter Scan Date = 2007-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 702826; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.22; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan
Description Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72512.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)
GSE11079 mRNAs associated with Ago2: Ago2, Ago2+miR-1, Ago2+miR-124, mock transfected
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 2705 9549 380 141 2325 9408 2935 11457 378 147 2555 11316 0 0 1154 4045 40 34 100 100 100 100 11733 13871 .247 4.046 4.429 4.81 3.893 1.831 12 104 3.869 .97 50 1470 5650 74 79 76 81 0 20913 309 20604 8.862 25092 24783 .113 9.7 3.148 3.278
2 2952 11695 369 141 2583 11554 3646 13633 371 144 3277 13492 0 0 1243 4295 37 22 100 100 100 100 14137 16769 .224 4.473 4.117 5.554 4.26 2.099 12 104 4.059 .96 50 1620 5650 74 79 91 96 0 25613 309 25304 9.796 29857 29549 .102 9.017 3.292 3.173
3 40289 35554 372 141 39917 35413 58943 37957 374 144 58571 37816 46 21 28641 26135 36 15 100 100 100 100 75330 96387 1.127 .887 .646 .922 .994 1.612 32 236 .891 .97 70 1770 5650 73 80 105 112 -100 77866 309 77557 1.943 83129 82820 .515 1.414 .958 .5
4 3731 13853 381 143 3350 13710 4242 13908 380 141 3861 13765 0 0 999 2943 38 12 100 100 100 100 17060 17626 .244 4.093 3.565 4.206 3.996 1.246 12 104 3.946 .97 50 1920 5650 74 79 121 126 0 30339 313 30026 8.963 30460 30146 .112 7.808 3.164 2.965
5 14753 11999 377 145 14376 11854 16900 13723 379 146 16523 13578 0 0 10437 8569 41 13 100 100 100 100 26230 30101 1.213 .825 .822 .8 .816 1.843 32 176 .817 .97 60 2070 5660 75 81 136 142 0 26279 318 25961 1.806 30054 29737 .554 1.8 .853 .848
6 44998 32042 375 145 44623 31897 58751 42703 379 147 58376 42558 3 0 22039 17676 42 14 100 100 100 100 76520 100934 1.399 .715 .729 .659 .722 1.384 32 232 .735 .98 70 2210 5660 74 81 149 156 0 70174 318 69857 1.565 93523 93205 .639 1.597 .647 .675
7 5499 5056 381 143 5118 4913 5852 5087 384 144 5471 4944 0 0 1024 575 43 11 100 100 100 100 10031 10415 1.042 .96 .904 .977 .934 1.189 12 104 .878 .96 50 2350 5650 74 79 164 169 0 11073 313 10760 2.102 11141 10828 .476 1.979 1.072 .985
8 41323 37102 380 149 40943 36953 50831 37594 380 151 50451 37445 40 21 26407 25962 43 15 100 100 100 100 77896 87896 1.108 .903 .742 .861 .924 1.99 32 176 .929 .95 60 2500 5660 75 81 179 185 -100 81256 326 80930 1.977 82334 82007 .506 1.625 .983 .701
9 2838 11220 367 147 2471 11073 3407 12869 368 149 3040 12722 0 0 1117 3163 37 19 100 100 100 100 13544 15762 .223 4.481 4.185 5.076 4.279 1.552 12 104 4.061 .95 50 2640 5650 74 79 193 198 0 24573 322 24251 9.814 28184 27862 .102 9.165 3.295 3.196
10 15466 14336 387 145 15079 14191 17438 16851 415 159 17051 16706 0 0 9378 7215 201 73 100 100 83 100 29270 33757 1.063 .941 .98 1.348 .851 2.473 12 104 .815 .95 50 2780 5650 74 79 207 212 0 31397 318 31079 2.061 36905 36587 .485 2.146 1.043 1.101
11 47228 47276 380 150 46848 47126 65321 56872 380 151 64941 56722 43 3 25518 20023 43 17 100 100 100 100 93974 121663 .994 1.006 .873 1.301 .975 2.09 32 236 .938 .97 70 2930 5650 73 80 221 228 -100 103538 329 103210 2.203 124554 124226 .454 1.913 1.14 .936
12 5003 4845 376 146 4627 4699 5785 5098 377 146 5409 4952 0 0 1607 758 38 12 100 100 100 100 9326 10361 .985 1.016 .916 1.085 .94 1.44 12 104 .874 .94 50 3080 5650 74 79 237 242 0 10611 320 10291 2.224 11165 10845 .45 2.005 1.153 1.004
13 768 339 387 146 381 193 801 340 382 145 414 194 0 0 107 36 38 11 100 100 100 100 574 608 1.974 .507 .469 .521 .505 1.417 12 68 .426 .89 40 3230 5650 75 79 253 257 0 742 320 423 1.109 745 425 .901 1.026 .15 .037
14 1505 262 386 144 1119 118 1653 272 385 144 1267 128 0 0 338 37 42 12 100 100 100 100 1237 1395 9.483 .105 .101 .106 .101 1.508 12 104 .096 .89 50 3370 5660 75 80 266 271 0 574 315 258 .231 596 280 4.33 .221 -2.114 -2.176
15 26753 3732 382 144 26371 3588 27184 3686 382 145 26802 3542 0 0 20335 2663 40 13 100 100 100 100 29959 30344 7.35 .136 .132 .151 .131 2.446 32 176 .128 .95 60 3520 5660 75 81 281 287 0 8173 315 7858 .298 8073 7757 3.356 .289 -1.747 -1.789
16 796 315 380 144 416 171 802 322 383 145 422 178 0 0 74 34 39 14 100 100 100 100 587 600 2.433 .411 .422 .409 .409 1.25 12 104 .377 .91 50 3670 5650 74 79 296 301 0 690 315 375 .9 705 390 1.111 .924 -.152 -.114
17 425 174 408 150 17 24 421 174 416 154 13 24 0 0 32 15 60 18 8 66 0 25 41 37 .708 1.412 1.846 1.009 .837 3.632 12 104 .251 .59 50 3810 5650 74 79 310 315 -50 381 329 53 3.092 381 53 .323 4.043 1.628 2.016
18 370 123 393 148 -23 -25 367 123 396 149 -26 -25 0 0 20 8 40 13 0 0 0 0 -48 -51 null null null 1.017 .949 1.871 12 104 .157 .36 50 3960 5650 74 79 325 330 -50 269 324 -55 2.381 269 -55 .42 2.106 1.251 1.074
19 7716 6448 372 147 7344 6301 9119 6918 380 146 8747 6771 0 0 3251 1405 42 11 100 100 100 100 13645 15518 1.166 .858 .774 .973 .788 1.609 12 104 .723 .94 50 4100 5650 74 79 339 344 0 14122 322 13800 1.879 15151 14829 .532 1.695 .91 .762
20 5509 4900 383 147 5126 4753 6281 5228 381 146 5898 5081 0 0 1488 761 37 12 100 100 100 100 9879 10979 1.078 .927 .861 .962 .886 1.286 12 104 .838 .96 50 4250 5650 74 79 354 359 0 10731 322 10409 2.031 11450 11128 .492 1.887 1.022 .916

Total number of rows: 49152

Table truncated, full table size 11021 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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