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Sample GSM466835 Query DataSets for GSM466835
Status Public on Nov 10, 2009
Title miR-124 12 hrs.C-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: miR-124 12 hrs.C-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/2008-07/80429.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
1 745 910 53 188 692 722 802 931 56 197 749 743 0 0 212 300 26 74 100 100 100 96 1414 1492 .958 1.043 .992 1.017 1.024 1.557 52 276 1.099 .91 80 1460 7030 208 216 120 128 0 1410 291 1119 1.617 1443 1151 .619 1.537 .693 .62
2 885 1065 54 211 831 854 937 989 66 217 883 778 0 0 223 365 82 97 98 100 96 100 1685 1661 .973 1.028 .881 1.01 .926 1.702 52 258 1.116 .9 90 1610 7030 207 216 134 143 0 1650 327 1323 1.593 1533 1206 .628 1.365 .671 .449
3 25156 28101 55 239 25101 27862 26285 28526 162 325 26230 28287 0 0 5771 7227 595 425 100 100 100 100 52963 54517 .901 1.11 1.078 1.098 1.092 1.105 52 299 1.131 .98 90 1760 7020 206 215 149 158 0 43546 370 43175 1.72 44204 43834 .581 1.671 .782 .741
4 1337 1461 54 213 1283 1248 1436 1512 74 244 1382 1299 0 0 381 585 137 154 100 90 92 90 2531 2681 1.028 .973 .94 .91 .918 1.393 52 294 1.079 .92 90 1900 7020 206 215 163 172 0 2264 330 1934 1.507 2343 2013 .663 1.457 .592 .543
5 2546 646 55 201 2491 445 2694 649 74 220 2639 448 0 0 579 197 98 112 100 94 100 88 2936 3087 5.598 .179 .17 .155 .172 2.018 52 226 .174 .85 80 2060 7020 207 215 180 188 0 1001 311 690 .277 1006 694 3.612 .263 -1.853 -1.927
6 19059 23052 53 192 19006 22860 22823 27011 63 206 22770 26819 0 0 6843 8507 72 82 100 100 100 100 41866 49589 .831 1.203 1.178 1.174 1.19 1.274 120 405 1.206 .99 120 2210 7000 203 215 193 205 0 35722 298 35424 1.864 41857 41559 .537 1.825 .898 .868
7 170 240 53 187 117 53 218 223 85 218 165 36 0 0 76 99 221 191 0 7 0 2 170 201 2.208 .453 .218 .712 .75 4.077 80 277 1.201 .52 100 2360 7000 204 214 209 219 0 372 290 82 .702 346 56 1.425 .338 -.511 -1.564
8 12951 13587 52 189 12899 13398 16656 16907 107 234 16604 16718 0 0 6789 6727 388 254 91 98 87 93 26297 33322 .963 1.039 1.007 1.299 1.021 2.371 80 304 1.025 .98 100 2510 7020 206 216 224 234 0 21055 293 20762 1.61 26199 25906 .621 1.56 .687 .642
9 50 156 50 177 0 -21 50 151 53 186 0 -26 0 0 3 61 15 71 0 7 0 1 -21 -26 null null null 15.467 15.5 3.069 52 253 173.488 .03 80 2670 7010 206 214 241 249 -50 242 274 -33 null 234 -40 0 null null null
10 65 151 50 177 15 -26 66 148 54 184 16 -29 0 0 5 53 36 84 0 3 0 0 -11 -13 null null null 2.582 2 2.845 52 243 82.411 .06 80 2820 7010 206 214 256 264 -50 234 274 -40 -2.686 229 -45 -.372 -2.809 null null
11 3787 5787 50 192 3737 5595 4093 6038 76 226 4043 5846 0 0 975 1512 149 235 100 100 98 98 9332 9889 .668 1.497 1.446 1.495 1.469 1.129 52 252 1.507 .98 80 2960 7010 206 214 270 278 0 8968 298 8670 2.32 9357 9059 .431 2.241 1.214 1.164
12 161 180 50 172 111 8 187 181 55 180 137 9 0 0 55 57 32 72 78 13 76 1 119 146 13.875 .072 .066 .407 .487 5.472 52 303 -6.538 -.03 90 3120 7000 204 213 285 294 0 279 267 12 .112 280 14 8.954 .102 -3.163 -3.296
13 2349 1656 51 181 2298 1475 2591 1719 66 193 2540 1538 0 0 704 500 122 105 98 92 96 92 3773 4078 1.558 .642 .606 .607 .619 1.52 52 227 .626 .95 80 3270 7010 206 214 301 309 0 2566 280 2286 .995 2664 2383 1.005 .938 -.008 -.092
14 233 366 51 186 182 180 251 350 53 197 200 164 0 0 56 123 12 80 94 76 92 50 362 364 1.011 .989 .82 .79 .889 4.117 52 272 2.002 .47 90 3420 7020 206 215 315 324 0 567 288 279 1.533 542 254 .652 1.271 .616 .346
15 44 145 50 173 -6 -28 44 148 53 181 -6 -25 0 0 5 59 22 78 0 3 0 0 -34 -31 null null null 6.284 8 2.703 52 232 24.119 .12 80 3570 7010 206 214 331 339 -50 225 268 -43 7.232 229 -39 .138 6.457 2.854 2.691
16 4400 1334 50 167 4350 1167 5170 1436 55 173 5120 1269 0 0 1744 520 24 73 100 96 100 92 5517 6389 3.728 .268 .248 .268 .27 1.668 52 271 .266 .94 80 3720 7000 205 213 346 354 0 2067 259 1808 .416 2225 1966 2.405 .384 -1.266 -1.381
17 104 154 51 161 53 -7 110 151 53 167 59 -10 0 0 19 56 13 61 90 11 90 5 46 49 null null null .946 .77 5.195 52 277 -19.401 -.09 80 3880 7010 206 214 362 370 100 239 249 -11 -.205 234 -15 -4.886 -.263 null null
18 45 150 51 165 -6 -15 45 138 57 167 -6 -27 0 0 4 59 29 65 0 7 0 5 -21 -33 null null null 5.985 7 3.158 52 217 -43.196 -.03 80 4030 7010 206 214 377 385 -50 232 256 -23 3.874 214 -42 .258 6.973 1.954 2.802
19 1073 2758 51 173 1022 2585 1163 2844 62 178 1112 2671 0 0 281 555 39 70 97 100 97 100 3607 3783 .395 2.529 2.402 2.873 2.455 1.978 80 320 2.533 .97 100 4160 7000 204 214 389 399 0 4274 268 4006 3.92 4407 4139 .255 3.722 1.971 1.896
20 9170 5430 50 171 9120 5259 9391 5435 53 181 9341 5264 0 0 1116 657 17 78 100 100 100 100 14379 14605 1.734 .577 .564 .579 .569 1.156 80 387 .563 .97 100 4310 6990 203 213 404 414 0 8414 265 8149 .894 8422 8157 1.119 .873 -.162 -.196

Total number of rows: 44544

Table truncated, full table size 9554 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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