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Sample GSM466847 Query DataSets for GSM466847
Status Public on Nov 10, 2009
Title miR-124 12 hrs.C-IP (5-20-08)
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 (5-20-08)
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/2008-07/80433.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 1581 1446 40 108 1541 1338 1609 1456 40 116 1569 1348 0 0 313 289 3 40 100 100 100 100 2879 2917 1.152 .868 .859 .867 .861 1.201 52 313 .889 .96 80 1490 6780 183 191 123 131 0 2126 159 1967 1.277 2141 1982 .783 1.263 .352 .337
2 1574 1436 40 109 1534 1327 1748 1571 42 116 1708 1462 0 0 543 429 18 42 98 100 98 100 2861 3170 1.156 .865 .856 .998 .864 1.809 52 240 .837 .98 80 1640 6790 184 192 138 146 0 2111 160 1951 1.272 2310 2150 .786 1.259 .347 .332
3 20035 24497 42 118 19993 24379 20738 25554 76 166 20696 25436 0 0 4706 4479 344 393 100 100 100 100 44372 46132 .82 1.219 1.229 1.252 1.202 1.257 52 312 1.186 .99 90 1790 6790 183 192 152 161 0 36019 174 35846 1.793 37573 37400 .558 1.807 .842 .854
4 1660 1370 40 117 1620 1253 1736 1375 72 157 1696 1258 0 0 302 334 342 390 98 98 98 94 2873 2954 1.293 .773 .742 .739 .766 1.322 52 316 .796 .97 90 1960 6780 182 191 169 178 0 2014 172 1842 1.137 2022 1850 .879 1.091 .186 .125
5 2122 675 41 113 2081 562 2286 656 45 117 2245 543 0 0 505 202 37 39 100 100 100 100 2643 2788 3.703 .27 .242 .266 .261 1.448 52 243 .263 .93 80 2100 6780 183 191 184 192 0 992 166 826 .397 965 798 2.518 .356 -1.332 -1.492
6 13694 15296 41 111 13653 15185 14796 17533 44 122 14755 17422 0 0 4727 5960 30 47 100 100 100 100 28838 32177 .899 1.112 1.181 1.079 1.139 1.194 80 338 1.136 .99 100 2260 6780 182 192 199 209 0 22490 163 22327 1.635 25780 25616 .611 1.736 .71 .796
7 266 219 41 113 225 106 276 195 42 120 235 82 0 0 37 76 7 60 100 73 100 32 331 317 2.123 .471 .349 .367 .42 2.294 52 263 .592 .7 80 2410 6770 182 190 215 223 0 322 166 156 .693 287 121 1.444 .513 -.53 -.963
8 17434 20957 42 122 17392 20835 19407 23661 42 136 19365 23539 0 0 7048 7586 4 70 100 100 100 100 38227 42904 .835 1.198 1.216 1.306 1.21 1.311 52 296 1.156 .99 90 2570 6780 182 191 230 239 0 30814 179 30635 1.761 34790 34611 .568 1.787 .817 .838
9 43 98 41 110 2 -12 43 93 41 116 2 -17 0 0 3 40 3 43 26 7 7 1 -10 -15 null null null 8.891 12.667 4.465 52 253 -315.648 -.04 80 2720 6780 183 191 246 254 -50 144 162 -18 -8.822 137 -25 -.113 -12.498 null null
10 62 109 40 113 22 -4 64 106 40 116 24 -7 0 0 6 36 3 38 100 13 94 3 18 17 null null null .963 1.643 2.999 52 248 -1 -1 80 2870 6780 183 191 261 269 -50 160 166 -6 -.267 156 -10 -3.741 -.429 null null
11 4029 6107 41 113 3988 5994 4285 6405 43 118 4244 6292 0 0 1155 1187 13 50 100 100 100 100 9982 10536 .665 1.503 1.483 1.564 1.501 1.226 52 258 1.446 .98 80 3010 6770 182 190 275 283 0 8979 166 8813 2.21 9418 9251 .452 2.18 1.144 1.124
12 176 137 41 110 135 27 195 138 42 113 154 28 0 0 50 44 10 37 92 40 92 17 162 182 5 .2 .182 .343 .366 3.854 52 288 .229 .28 80 3160 6760 181 189 290 298 0 201 162 40 .294 203 41 3.401 .267 -1.766 -1.903
13 2571 1711 41 117 2530 1594 2581 1739 42 118 2540 1622 0 0 148 268 10 39 100 100 100 100 4124 4162 1.587 .63 .639 .622 .624 1.177 32 217 .628 .97 70 3310 6770 182 189 305 312 0 2516 172 2344 .926 2557 2385 1.079 .939 -.11 -.091
14 213 236 41 111 172 125 220 239 42 114 179 128 0 0 25 70 9 38 100 92 100 71 297 307 1.376 .727 .715 .702 .804 1.701 52 282 .977 .73 80 3480 6770 182 190 322 330 0 347 163 184 1.069 351 188 .936 1.051 .096 .072
15 39 92 41 112 -2 -20 39 85 41 114 -2 -27 0 0 3 36 3 35 3 3 0 3 -22 -29 null null null 6.932 8.75 3.886 52 249 69.296 .19 80 3620 6780 183 191 336 344 -50 135 165 -29 14.703 125 -40 .068 19.85 3.878 4.311
16 4554 1602 41 115 4513 1487 4611 1604 41 118 4570 1489 0 0 844 358 3 36 100 100 100 100 6000 6059 3.035 .329 .326 .327 .32 1.156 52 268 .325 .98 90 3780 6780 182 191 351 360 0 2355 169 2186 .484 2358 2189 2.064 .479 -1.046 -1.062
17 69 117 41 108 28 9 46 117 41 112 5 9 0 0 32 35 3 36 54 17 49 6 37 14 3.111 .321 1.8 1.47 1.204 6.806 120 435 37.561 .03 120 3930 6790 182 194 365 377 0 172 159 13 .473 172 13 2.116 2.647 -1.081 1.404
18 40 102 41 103 -1 -1 41 94 41 109 0 -9 0 0 3 37 3 36 5 15 1 5 -2 -9 null null null 7.565 8.5 2.838 52 222 -108.077 -.1 80 4070 6780 183 191 381 389 -50 150 151 -1 1.47 138 -13 .68 null .556 null
19 2111 3500 41 112 2070 3388 2141 3576 41 116 2100 3464 0 0 389 700 3 40 100 100 100 100 5458 5564 .611 1.637 1.65 1.619 1.65 1.144 80 338 1.637 .99 100 4230 6770 181 191 396 406 0 5146 165 4982 2.407 5258 5093 .416 2.425 1.267 1.278
20 9788 7252 41 113 9747 7139 9754 7532 41 118 9713 7419 0 0 2295 1619 3 41 100 100 100 100 16886 17132 1.365 .732 .764 .735 .745 1.17 80 326 .724 .99 100 4380 6770 181 191 411 421 0 10663 166 10497 1.077 11075 10909 .929 1.123 .107 .167

Total number of rows: 44544

Table truncated, full table size 9460 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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