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Sample GSM466849 Query DataSets for GSM466849
Status Public on Nov 10, 2009
Title miR-124 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: miR-124 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/2008-07/80423.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 1210 1691 59 64 1151 1627 1218 1683 62 66 1159 1619 0 0 114 112 26 25 100 100 100 100 2778 2778 .707 1.414 1.397 1.417 1.416 1.074 32 236 1.387 .99 70 1470 6860 191 198 121 128 0 2998 113 2885 2.507 2984 2871 .399 2.477 1.326 1.309
2 1142 1565 62 67 1080 1498 1223 1691 64 68 1161 1624 0 0 231 339 14 10 100 100 100 100 2578 2785 .721 1.387 1.399 1.384 1.413 1.144 52 272 1.387 .99 80 1630 6860 191 199 137 145 0 2775 119 2656 2.459 2998 2880 .407 2.48 1.298 1.311
3 18345 15968 64 74 18281 15894 21818 19074 68 76 21754 19000 0 0 6461 5898 17 13 100 100 100 100 34175 40754 1.15 .869 .873 .858 .879 1.284 52 264 .876 .99 80 1780 6850 190 198 152 160 0 28314 131 28183 1.542 33822 33691 .649 1.549 .624 .631
4 1120 1570 64 74 1056 1496 1176 1703 66 75 1112 1629 0 0 234 296 15 11 100 100 100 100 2552 2741 .706 1.417 1.465 1.432 1.424 1.143 52 267 1.407 .99 80 1930 6850 190 198 167 175 0 2784 131 2653 2.512 3020 2889 .398 2.598 1.329 1.377
5 6279 3285 69 81 6210 3204 5682 3208 271 158 5613 3127 0 0 1296 465 711 273 100 100 100 100 9414 8740 1.938 .516 .557 .521 .546 1.125 52 236 .485 .98 90 2100 6850 189 198 183 192 0 5825 144 5681 .915 5688 5545 1.093 .988 -.128 -.018
6 19388 14077 74 91 19314 13986 20958 15429 281 161 20884 15338 0 0 3120 2939 681 259 100 100 100 100 33300 36222 1.381 .724 .734 .714 .738 1.097 52 260 .729 .99 90 2220 6850 189 198 195 204 0 24961 161 24800 1.284 27359 27197 .779 1.302 .361 .381
7 412 182 69 82 343 100 427 184 78 85 358 102 0 0 62 24 51 17 100 100 100 98 443 460 3.43 .292 .285 .285 .288 1.22 52 274 .285 .95 80 2390 6850 190 198 213 221 0 323 145 177 .517 326 181 1.934 .505 -.952 -.985
8 18840 16360 70 85 18770 16275 21543 18790 74 86 21473 18705 0 0 5344 5231 16 12 100 100 100 100 35045 40178 1.153 .867 .871 .844 .879 1.166 52 221 .879 .99 80 2540 6850 190 198 228 236 0 29010 151 28859 1.537 33318 33168 .65 1.545 .621 .627
9 56 57 68 81 -12 -24 56 51 69 82 -12 -30 0 0 9 18 10 10 1 3 0 3 -36 -42 null null null 2.238 2.24 1.692 52 223 .858 .48 80 2680 6850 190 198 242 250 -50 101 144 -43 3.546 90 -53 .282 4.433 1.826 2.148
10 91 63 70 85 21 -22 90 58 71 90 20 -27 0 0 9 15 7 49 94 0 76 0 -1 -7 null null null .812 .548 3.027 52 218 -2.286 -.4 80 2830 6850 190 198 257 265 -50 112 151 -39 -1.858 103 -48 -.538 -2.394 null null
11 7324 7089 73 90 7251 6999 7856 7612 76 95 7783 7522 0 0 1609 1326 15 50 100 100 100 100 14250 15305 1.036 .965 .966 .977 .966 1.127 52 234 .95 .99 80 2980 6850 190 198 272 280 0 12570 160 12411 1.712 13498 13338 .584 1.714 .775 .777
12 323 106 72 88 251 18 346 106 73 88 274 18 0 0 60 12 8 11 100 63 100 32 269 292 13.944 .072 .066 .061 .071 2.025 52 248 .075 .61 80 3140 6840 189 197 288 296 0 188 156 32 .127 188 32 7.864 .116 -2.975 -3.102
13 5033 6770 74 91 4959 6679 5265 7207 74 90 5191 7116 0 0 971 1278 8 11 100 100 100 100 11638 12307 .742 1.347 1.371 1.349 1.364 1.128 52 258 1.346 .99 80 3290 6840 189 197 303 311 0 12005 161 11843 2.388 12779 12618 .419 2.431 1.256 1.281
14 479 1072 75 92 404 980 524 1168 75 92 449 1076 0 0 112 224 8 11 100 100 100 100 1384 1525 .412 2.426 2.396 2.48 2.446 1.172 52 227 2.39 .99 80 3440 6850 190 198 318 326 0 1901 163 1738 4.301 2071 1908 .232 4.249 2.105 2.087
15 50 52 76 93 -26 -41 46 45 77 95 -30 -48 0 0 12 17 9 13 0 0 0 0 -67 -78 null null null 1.635 1.571 1.587 52 246 1.623 .82 80 3590 6850 190 198 333 341 -50 92 165 -73 2.796 80 -85 .358 2.837 1.483 1.504
16 10903 2749 80 99 10823 2650 10716 2732 83 100 10636 2633 0 0 544 142 14 14 100 100 100 100 13473 13269 4.084 .245 .248 .245 .245 1.039 32 221 .239 .99 70 3740 6840 189 196 348 355 0 4875 176 4699 .434 4844 4669 2.303 .439 -1.204 -1.188
17 188 119 78 96 110 23 197 118 80 98 119 22 0 0 26 12 11 12 100 88 100 44 133 141 4.783 .209 .185 .208 .212 1.624 52 272 .177 .57 80 3890 6840 189 197 363 371 0 211 170 41 .371 209 39 2.697 .328 -1.431 -1.609
18 53 59 78 99 -25 -40 44 44 80 100 -34 -55 0 0 17 28 11 15 0 3 0 0 -65 -89 null null null 1.77 1.62 1.508 52 245 1.524 .77 80 4050 6850 190 198 379 387 -50 105 176 -71 2.837 78 -98 .352 2.868 1.504 1.52
19 3140 15954 84 107 3056 15847 3164 16746 86 112 3080 16639 0 0 382 2727 12 26 100 100 100 100 18903 19719 .193 5.186 5.402 5.122 5.334 1.112 52 279 5.274 .99 90 4200 6840 188 197 393 402 0 28290 190 28100 9.195 29694 29504 .109 9.579 3.201 3.26
20 18518 8748 96 118 18422 8630 20148 9450 143 129 20052 9332 0 0 4078 1579 157 48 100 100 100 100 27052 29384 2.135 .468 .465 .475 .467 1.142 52 271 .46 .99 80 4340 6840 189 197 408 416 0 15512 209 15303 .831 16757 16548 1.204 .825 -.268 -.277

Total number of rows: 44544

Table truncated, full table size 9579 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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