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Sample GSM466845 Query DataSets for GSM466845
Status Public on Nov 10, 2009
Title mock 12 hrs.IP (5-12-08)
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.IP (5-12-08)
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/2008-07/80422.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
1 921 1360 42 45 879 1315 949 1433 42 45 907 1388 0 0 143 257 5 7 100 100 100 100 2194 2295 .668 1.496 1.53 1.482 1.531 1.122 52 343 1.49 .99 90 1500 6860 190 199 123 132 0 2467 82 2385 2.713 2599 2518 .369 2.776 1.44 1.473
2 912 1425 42 47 870 1378 965 1519 100 67 923 1472 0 0 195 276 133 48 98 100 96 100 2248 2395 .631 1.584 1.595 1.617 1.608 1.167 52 256 1.604 .97 80 1650 6850 190 198 139 147 0 2585 85 2499 2.873 2755 2670 .348 2.893 1.522 1.532
3 14087 12404 44 50 14043 12354 14767 13349 103 80 14723 13299 0 0 2347 2540 134 78 100 100 100 100 26397 28022 1.137 .88 .903 .869 .907 1.162 52 319 .893 .99 90 1810 6850 189 198 154 163 0 22498 91 22407 1.596 24212 24121 .627 1.638 .674 .712
4 901 1362 42 48 859 1314 937 1457 49 57 895 1409 0 0 137 283 32 57 100 100 100 100 2173 2304 .654 1.53 1.574 1.501 1.552 1.132 52 302 1.562 .99 90 1960 6850 189 198 169 178 0 2470 87 2383 2.774 2643 2556 .36 2.855 1.472 1.514
5 2391 1916 43 50 2348 1866 2538 2009 48 53 2495 1959 0 0 405 300 17 14 100 100 100 100 4214 4454 1.258 .795 .785 .8 .797 1.115 52 274 .794 .99 90 2100 6850 189 198 183 192 0 3475 91 3384 1.441 3644 3553 .694 1.424 .528 .51
6 11565 12779 44 53 11521 12726 12329 13706 176 126 12285 13653 0 0 1949 2347 518 282 100 100 100 100 24247 25938 .905 1.105 1.111 1.104 1.115 1.144 80 322 1.113 .99 100 2240 6850 189 199 197 207 0 23178 96 23082 2.003 24859 24763 .499 2.016 1.002 1.011
7 3741 2362 284 235 3457 2127 3621 2361 787 471 3337 2126 0 0 349 226 1041 556 100 100 100 100 5584 5463 1.625 .615 .637 .615 .614 1.084 12 56 .618 .96 40 2350 6840 191 195 211 215 -100 4284 426 3858 1.116 4282 3856 .896 1.156 .158 .209
8 13962 12280 44 59 13918 12221 14875 13523 97 118 14831 13464 0 0 2674 3138 403 479 100 100 100 100 26139 28295 1.139 .878 .908 .852 .914 1.209 52 320 .892 .99 90 2560 6840 188 197 229 238 0 22273 107 22166 1.593 24527 24420 .628 1.647 .671 .719
9 47 49 43 56 4 -7 47 47 44 57 4 -9 0 0 4 10 4 8 42 9 5 3 -3 -5 null null null 3.92 3 2.429 52 211 -73.476 -.03 80 2690 6860 191 199 243 251 -50 89 102 -13 -3.174 85 -16 -.315 -4.081 null null
10 66 64 43 57 23 7 67 57 43 58 24 0 0 0 8 21 3 8 94 26 92 23 30 24 3.286 .304 null .558 .623 3.188 52 320 3.955 .09 90 2840 6840 188 197 257 266 0 116 103 13 .552 103 0 1.812 0 -.857 null
11 3959 7303 45 62 3914 7241 4106 7635 47 65 4061 7573 0 0 499 960 12 21 100 100 100 100 11155 11634 .541 1.85 1.865 1.849 1.869 1.122 52 270 1.853 .98 80 3000 6840 189 197 274 282 0 13246 112 13133 3.356 13848 13736 .298 3.382 1.747 1.758
12 233 149 44 63 189 86 233 98 46 65 189 35 0 0 43 98 8 13 100 92 100 62 275 224 2.198 .455 .185 .261 .204 2.607 80 352 .699 .66 100 3150 6840 188 198 288 298 0 270 114 156 .825 178 63 1.212 .336 -.277 -1.574
13 3070 1430 45 64 3025 1366 3296 1528 48 66 3251 1464 0 0 625 255 11 11 100 100 100 100 4391 4715 2.214 .452 .45 .456 .451 1.166 52 251 .442 .99 80 3300 6840 189 197 304 312 0 2594 116 2478 .819 2771 2655 1.221 .817 -.288 -.292
14 340 281 45 66 295 215 360 294 49 68 315 228 0 0 57 51 11 11 100 100 100 100 510 543 1.372 .729 .724 .719 .733 1.19 52 255 .754 .97 80 3460 6840 189 197 320 328 0 510 120 390 1.322 533 414 .756 1.313 .403 .393
15 40 48 46 69 -6 -21 40 45 46 70 -6 -24 0 0 4 11 3 11 1 1 0 0 -27 -30 null null null 3.704 3.67 1.767 52 241 5.822 .62 80 3600 6850 190 198 334 342 -50 87 125 -38 6.348 82 -44 .158 7.255 2.666 2.859
16 5053 1666 47 77 5006 1589 5590 1891 48 78 5543 1814 0 0 1280 482 7 13 100 100 100 100 6595 7357 3.15 .317 .327 .302 .322 1.357 52 282 .32 .99 80 3750 6830 188 196 349 357 0 3022 140 2882 .576 3430 3290 1.737 .594 -.797 -.753
17 300 100 49 89 251 11 321 97 49 91 272 8 0 0 65 14 4 14 100 32 100 9 262 280 22.818 .044 .029 .038 .041 3.01 52 267 .029 .2 80 3910 6840 189 197 365 373 0 181 161 20 .079 176 15 12.581 .053 -3.653 -4.228
18 43 57 50 90 -7 -33 42 49 51 95 -8 -41 0 0 5 20 10 25 0 0 0 0 -40 -49 null null null 3.97 4.364 1.733 52 255 6.308 .72 80 4050 6850 190 198 379 387 -50 103 163 -60 8.551 89 -74 .117 9.296 3.096 3.217
19 1993 4381 51 89 1942 4292 2059 4529 63 98 2008 4440 0 0 285 521 87 43 100 100 100 100 6234 6448 .452 2.21 2.211 2.223 2.214 1.113 52 283 2.242 .98 90 4210 6840 188 197 394 403 0 7946 161 7785 4.009 8215 8053 .249 4.011 2.003 2.004
20 10694 6501 50 88 10644 6413 11223 6823 61 92 11173 6735 0 0 2060 935 88 36 100 100 100 100 17057 17908 1.66 .602 .603 .614 .601 1.161 52 269 .595 .99 90 4360 6840 188 197 409 418 0 11791 160 11632 1.093 12375 12216 .915 1.093 .128 .129

Total number of rows: 44544

Table truncated, full table size 9564 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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