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Sample GSM466859 Query DataSets for GSM466859
Status Public on Nov 10, 2009
Title mir-124 12 hrs SS (5-14-08)
Sample type RNA
 
Channel 1
Source name universal reference
Organism Homo sapiens
Characteristics reference: universal reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name mir-124 12 hrs SS (5-14-08) (aRNA)
Organism Homo sapiens
Characteristics cell line: HEK293T
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/2008-07/80599.gif
Measurement: concentration(absolute) 60 nM
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)
GSE18835 mRNA abundance in HEK293T cells mock or miR-124 transfected
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 13940 32086 99 84 13841 32002 16056 35373 101 90 15957 35289 0 0 4588 8299 18 28 100 100 100 100 45843 51246 .433 2.312 2.212 2.488 2.244 1.307 52 343 2.238 .99 90 1650 7090 180 189 152 161 0 53567 140 53427 3.86 59055 58915 .259 3.692 1.949 1.884
2 15601 36050 100 86 15501 35964 16663 37443 103 92 16563 37357 0 0 3122 5351 18 27 100 100 100 100 51465 53920 .431 2.32 2.255 2.363 2.275 1.121 52 270 2.299 1 90 1810 7090 180 189 168 177 0 60185 144 60042 3.873 62511 62367 .258 3.765 1.954 1.913
3 15373 50877 99 89 15274 50788 17712 56618 137 123 17613 56529 0 0 5240 13442 160 151 100 100 98 100 66062 74142 .301 3.325 3.21 3.686 3.229 1.493 52 276 3.256 .99 90 1960 7090 180 189 183 192 0 84939 149 84790 5.551 94524 94375 .18 5.358 2.473 2.422
4 15422 35764 101 86 15321 35678 16739 37510 137 121 16638 37424 0 0 3110 5688 162 153 100 100 100 100 50999 54062 .429 2.329 2.249 2.367 2.288 1.125 52 262 2.306 .99 80 2110 7080 180 188 199 207 0 59708 144 59564 3.888 62623 62479 .257 3.755 1.959 1.909
5 4998 11451 98 83 4900 11368 5294 12271 103 88 5196 12188 0 0 932 2415 28 27 100 100 100 100 16268 17384 .431 2.32 2.346 2.303 2.325 1.079 52 224 2.344 .99 80 2270 7080 180 188 215 223 0 19117 139 18979 3.873 20486 20348 .258 3.916 1.954 1.969
6 17442 50740 99 83 17343 50657 18222 56012 105 93 18123 55929 0 0 2175 11476 39 38 100 100 100 100 68000 74052 .342 2.921 3.086 2.855 2.995 1.183 80 341 3.024 .99 110 2400 7080 178 189 226 237 0 84710 139 84572 4.876 93512 93373 .205 5.152 2.286 2.365
7 828 1015 100 87 728 928 874 1021 108 100 774 934 0 0 168 170 35 53 100 100 100 100 1656 1708 .784 1.275 1.207 1.301 1.277 1.166 52 258 1.253 .99 80 2560 7080 180 188 244 252 0 1695 145 1549 2.128 1705 1559 .47 2.015 1.09 1.011
8 13421 45209 98 87 13323 45122 16245 57573 104 97 16147 57486 0 0 5881 20482 25 44 100 100 100 100 58445 73633 .295 3.387 3.56 3.18 3.295 1.286 80 344 3.444 .99 100 2720 7080 179 189 259 269 0 75476 145 75331 5.654 96118 95973 .177 5.944 2.499 2.571
9 624 175 97 86 527 89 643 177 101 91 546 91 0 0 95 29 17 22 100 100 100 94 616 637 5.921 .169 .167 .163 .161 1.356 52 228 .159 .84 80 2860 7080 180 188 274 282 0 292 144 149 .282 296 152 3.547 .278 -1.827 -1.846
10 316 224 98 85 218 139 321 227 102 89 223 142 0 0 56 39 17 21 100 100 100 100 357 365 1.568 .638 .637 .636 .643 1.239 52 226 .611 .95 80 3010 7070 179 187 289 297 0 374 142 232 1.064 379 237 .939 1.063 .09 .088
11 9239 26123 98 85 9141 26038 9752 27510 101 91 9654 27425 0 0 2520 6067 19 24 100 100 100 100 35179 37079 .351 2.848 2.841 2.965 2.812 1.235 52 283 2.79 1 90 3150 7070 178 187 302 311 0 43612 142 43470 4.756 45928 45786 .21 4.743 2.25 2.246
12 875 1240 97 81 778 1159 908 1275 99 86 811 1194 0 0 130 185 16 18 100 100 100 100 1937 2005 .671 1.49 1.472 1.492 1.51 1.111 52 291 1.485 .99 90 3310 7080 179 188 318 327 0 2070 135 1935 2.487 2129 1993 .402 2.458 1.314 1.297
13 5826 13212 94 81 5732 13131 6132 13908 95 83 6038 13827 0 0 1067 2685 16 16 100 100 100 100 18863 19865 .437 2.291 2.29 2.278 2.309 1.103 52 253 2.311 .99 80 3460 7070 179 187 334 342 0 22057 135 21922 3.825 23219 23084 .261 3.823 1.935 1.935
14 2709 1559 94 80 2615 1479 2814 1626 95 83 2720 1546 0 0 336 230 14 16 100 100 100 100 4094 4266 1.768 .566 .568 .563 .566 1.083 52 258 .565 .99 80 3610 7080 180 188 349 357 0 2603 134 2469 .944 2715 2581 1.059 .949 -.083 -.076
15 83 61 96 83 -13 -22 82 58 99 88 -14 -25 0 0 12 13 17 21 0 0 0 0 -35 -39 null null null 1.535 1.412 2.144 52 242 1.391 .6 80 3770 7080 180 188 365 373 -50 102 139 -37 null 97 -42 null null null null
16 16139 22214 95 82 16044 22132 17067 23762 98 86 16972 23680 0 0 2812 4532 15 19 100 100 100 100 38176 40652 .725 1.379 1.395 1.369 1.402 1.107 52 241 1.391 .99 80 3910 7070 179 187 379 387 0 37086 137 36949 2.303 39671 39534 .434 2.329 1.204 1.22
17 3541 1093 93 80 3448 1013 3709 1141 96 83 3616 1061 0 0 536 173 13 18 100 100 100 100 4461 4677 3.404 .294 .293 .293 .289 1.115 52 246 .29 .99 80 4060 7070 179 187 394 402 0 1825 134 1691 .49 1905 1771 2.039 .49 -1.028 -1.03
18 82 68 95 82 -13 -14 79 61 98 85 -16 -21 0 0 15 20 15 17 5 7 1 1 -27 -37 null null null 1.336 1.208 2.132 52 230 1.501 .66 80 4220 7080 180 188 410 418 -50 114 137 -23 null 102 -35 null null null null
19 17543 12592 96 83 17447 12509 17795 12893 109 91 17699 12810 0 0 1467 1403 73 34 100 100 100 100 29956 30509 1.395 .717 .724 .714 .727 1.065 52 267 .72 .99 90 4370 7070 178 187 424 433 0 21022 139 20884 1.197 21525 21386 .835 1.208 .259 .273
20 19189 52377 98 87 19091 52290 20543 54330 115 99 20445 54243 0 0 3483 7792 72 50 100 100 100 100 71381 74688 .365 2.739 2.653 2.773 2.735 1.15 52 284 2.718 .99 90 4510 7060 177 186 438 447 0 87443 145 87298 4.573 90704 90559 .219 4.429 2.193 2.147

Total number of rows: 44544

Table truncated, full table size 9734 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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