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Sample GSM466844 Query DataSets for GSM466844
Status Public on Nov 10, 2009
Title mock 12 hrs.C-IP (5-14-08)
Sample type RNA
 
Channel 1
Source name total cell lysate aRNA
Organism Homo sapiens
Characteristics reference: total cell lysate
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name immunoprecipitated aRNA
Organism Homo sapiens
Characteristics experiment: mock 12 hrs.C-IP (5-14-08)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix
Description Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80430.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 Oct 30, 2009
Last update date Nov 06, 2009
Contact name Patrick O Brown
E-mail(s) pbrown@cmgm.stanford.edu
Organization name Stanford university school of medicine
Department Department of biochemistry
Street address Beckman Center b439
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL9497
Series (2)
GSE18834 Human Argonaute Immunoaffinity Purification-associated RNA
GSE18889 Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

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 1130 1145 47 199 1083 946 1245 1136 48 215 1198 937 0 0 329 344 8 90 100 96 100 96 2029 2135 1.145 .873 .782 .922 .842 1.56 52 309 .883 .92 80 1480 7150 220 228 122 130 0 1694 294 1400 1.292 1681 1386 .774 1.157 .37 .211
2 1182 1210 47 209 1135 1001 1238 1213 48 225 1191 1004 0 0 163 293 9 100 100 100 100 100 2136 2195 1.134 .882 .843 .856 .891 1.33 52 257 .929 .94 90 1630 7150 219 228 136 145 0 1790 309 1481 1.305 1795 1485 .766 1.247 .384 .319
3 20891 23359 48 228 20843 23131 22147 24765 118 309 22099 24537 0 0 3390 4260 601 596 100 100 100 100 43974 46636 .901 1.11 1.11 1.103 1.105 1.121 52 305 1.108 .99 90 1760 7140 218 227 149 158 0 34560 337 34223 1.642 36640 36303 .609 1.643 .715 .716
4 1119 1169 47 208 1072 961 1168 1131 73 232 1121 923 0 0 148 313 169 181 100 100 100 100 2033 2044 1.116 .896 .823 .861 .859 1.333 52 315 .959 .93 90 1940 7150 219 228 167 176 0 1730 308 1422 1.326 1673 1366 .754 1.218 .407 .285
5 1637 534 47 206 1590 328 1736 522 50 220 1689 316 0 0 260 153 24 87 100 98 100 86 1918 2005 4.848 .206 .187 .183 .202 1.905 52 266 .205 .78 90 2090 7140 218 227 182 191 0 790 305 485 .305 772 468 3.276 .277 -1.712 -1.853
6 10954 11760 47 216 10907 11544 13369 13245 48 228 13322 13029 0 0 3795 4304 7 94 100 100 100 100 22451 26351 .945 1.058 .978 1.05 1.063 1.11 80 338 1.054 .99 100 2220 7140 218 228 195 205 0 17399 320 17080 1.566 19596 19277 .639 1.447 .647 .533
7 192 256 48 216 144 40 199 248 108 274 151 32 0 0 30 116 486 432 0 0 0 0 184 183 3.6 .278 .212 .551 .591 2.292 32 227 3.579 .21 70 2380 7130 218 225 212 219 100 379 320 59 .411 367 47 2.433 .314 -1.283 -1.673
8 15570 19015 48 215 15522 18800 15877 20337 115 290 15829 20122 0 0 4386 5279 521 516 100 100 98 100 34322 35951 .826 1.211 1.271 1.244 1.211 1.24 52 318 1.196 .99 90 2540 7130 217 226 227 236 0 28133 318 27815 1.792 30089 29771 .558 1.881 .842 .911
9 46 216 47 201 -1 15 47 208 47 204 0 7 0 0 3 76 3 87 6 18 0 3 14 7 null null null 19.224 24.7 3.911 32 228 -1 -1 70 2690 7130 218 225 243 250 -50 320 297 22 -22.193 308 10 -.045 null null null
10 61 174 46 183 15 -9 61 169 47 198 15 -14 0 0 6 87 4 89 93 15 84 3 6 1 null null null 3.513 3.667 5.581 32 222 -75.93 -.13 70 2840 7130 218 225 258 265 -50 257 271 -13 -.888 250 -21 -1.126 -1.381 null null
11 3136 4823 46 189 3090 4634 3043 4862 47 202 2997 4673 0 0 418 671 8 83 100 100 100 100 7724 7670 .667 1.5 1.559 1.498 1.513 1.127 52 342 1.478 .98 90 2980 7130 217 226 271 280 0 7136 280 6856 2.219 7193 6914 .451 2.307 1.15 1.206
12 151 159 46 195 105 -36 156 133 50 202 110 -62 0 0 23 89 15 82 96 15 96 3 69 48 null null null .694 1.032 3.341 32 180 -8.49 -.15 70 3140 7130 218 225 288 295 100 235 289 -53 -.507 197 -92 -1.971 -.834 null null
13 1636 1222 47 179 1589 1043 1892 1309 49 189 1845 1130 0 0 594 431 31 80 94 98 94 94 2632 2975 1.523 .656 .612 .746 .642 2.226 52 237 .635 .94 80 3260 7130 218 226 300 308 0 1808 265 1543 .971 1937 1672 1.03 .906 -.042 -.142
14 186 288 46 180 140 108 229 282 47 192 183 102 0 0 89 114 20 79 78 60 76 31 248 285 1.296 .771 .557 1.143 .899 4.176 120 588 1.643 .49 120 3440 7120 215 227 316 328 0 426 266 160 1.141 417 151 .876 .825 .191 -.278
15 44 161 46 190 -2 -29 44 152 46 200 -2 -38 0 0 3 64 7 80 0 6 0 0 -31 -40 null null null 17.441 15 2.453 32 202 105.049 .22 70 3600 7130 218 225 334 341 -50 238 281 -43 21.453 225 -56 .047 28.111 4.423 4.813
16 3495 1119 46 206 3449 913 3756 1178 49 208 3710 972 0 0 789 304 38 83 100 98 98 98 4362 4682 3.778 .265 .262 .259 .269 1.378 52 326 .258 .93 90 3730 7120 216 225 346 355 0 1656 305 1351 .392 1743 1438 2.553 .388 -1.352 -1.367
17 185 196 46 185 139 11 222 182 48 193 176 -3 0 0 73 85 35 81 78 19 75 5 150 173 12.636 .079 null .579 .488 5.795 52 364 -1 -1 90 3880 7120 216 225 361 370 0 290 274 16 .117 269 -4 8.541 -.025 -3.094 null
18 46 262 45 159 1 103 46 261 45 164 1 102 0 0 4 72 4 72 16 75 0 33 104 103 .01 103 102 22.735 23.625 3.272 12 53 378.676 .06 40 4090 7110 218 222 385 389 -100 388 235 152 152.391 386 151 .007 150.911 7.252 7.238
19 1289 2329 47 191 1242 2138 1305 2360 65 211 1258 2169 0 0 101 346 112 127 100 100 100 100 3380 3427 .581 1.721 1.724 1.706 1.766 1.169 52 276 1.73 .96 90 4180 7120 216 225 391 400 0 3446 283 3163 2.547 3492 3209 .393 2.551 1.349 1.351
20 8100 6453 48 198 8052 6255 8513 6548 69 229 8465 6350 0 0 1456 1106 142 174 100 100 100 100 14307 14815 1.287 .777 .75 .786 .794 1.19 52 335 .76 .97 90 4350 7120 216 225 408 417 0 9547 293 9254 1.149 9688 9395 .87 1.11 .201 .15

Total number of rows: 44544

Table truncated, full table size 9566 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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