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Sample GSM466857 Query DataSets for GSM466857
Status Public on Nov 10, 2009
Title mock 12 hrs SS (5-12-08)
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 mock 12 hrs SS (5-12-08) (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/2008-07/80596.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)
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 12255 16040 101 75 12154 15965 12866 16363 103 78 12765 16288 0 0 1754 1817 19 16 100 100 100 100 28119 29053 .761 1.314 1.276 1.323 1.302 1.149 52 323 1.315 .99 90 1550 6950 166 175 142 151 0 25316 118 25198 2.073 25826 25707 .482 2.014 1.052 1.01
2 11324 8080 98 70 11226 8010 11950 7889 102 77 11852 7819 0 0 2157 1339 31 39 100 100 100 100 19236 19671 1.401 .714 .66 .726 .688 1.219 52 274 .708 .98 90 1700 6950 166 175 157 166 0 12753 110 12642 1.126 12451 12341 .888 1.041 .171 .058
3 11246 13448 95 67 11151 13381 12341 14540 102 78 12246 14473 0 0 2605 2425 41 56 100 100 100 100 24532 26719 .833 1.2 1.182 1.222 1.169 1.12 52 242 1.162 .99 80 1860 6950 167 175 174 182 0 21225 106 21119 1.894 22949 22843 .528 1.865 .921 .899
4 12271 6663 92 64 12179 6599 12667 6936 94 65 12575 6872 0 0 1440 672 18 11 100 100 100 100 18778 19447 1.846 .542 .546 .544 .547 1.098 52 226 .537 .99 90 2010 6950 166 175 188 197 0 10516 101 10415 .855 10947 10846 1.169 .863 -.226 -.213
5 3393 5619 91 63 3302 5556 3891 6306 91 63 3800 6243 0 0 1081 1524 10 9 100 100 100 100 8858 10043 .594 1.683 1.643 1.795 1.644 1.284 52 209 1.641 .99 80 2150 6940 166 174 203 211 0 8868 99 8769 2.656 9953 9853 .377 2.593 1.409 1.375
6 13636 13377 91 63 13545 13314 15688 15731 94 65 15597 15668 0 0 3570 3758 26 13 100 100 100 100 26859 31265 1.017 .983 1.005 .975 .997 1.075 80 330 .985 1 100 2310 6940 165 175 218 228 0 21113 99 21014 1.551 24828 24729 .645 1.585 .634 .665
7 631 524 91 63 540 461 707 576 101 75 616 513 0 0 172 125 65 120 96 94 94 92 1001 1129 1.171 .854 .833 .899 .847 1.252 52 291 .832 .99 90 2450 6940 165 174 232 241 0 827 99 728 1.347 909 810 .742 1.314 .43 .394
8 12401 14582 92 63 12309 14519 13304 15551 98 80 13212 15488 0 0 2576 2697 54 137 100 100 100 100 26828 28700 .848 1.18 1.172 1.197 1.171 1.101 52 306 1.156 1 90 2610 6940 165 174 248 257 0 23015 99 22915 1.862 24544 24445 .537 1.85 .897 .888
9 444 87 92 61 352 26 467 86 92 62 375 25 0 0 77 10 10 6 100 96 100 90 378 400 13.538 .074 .067 .069 .072 1.525 52 255 .068 .85 80 2760 6940 166 174 264 272 0 137 96 41 .117 136 39 8.578 .105 -3.101 -3.249
10 235 114 92 62 143 52 241 114 92 63 149 52 0 0 29 14 10 12 100 100 100 96 195 201 2.75 .364 .349 .362 .358 1.266 52 218 .362 .94 80 2910 6950 167 175 279 287 0 180 98 82 .574 180 82 1.742 .551 -.801 -.86
11 5875 7971 91 62 5784 7909 5982 8303 92 63 5891 8241 0 0 499 1002 10 12 100 100 100 100 13693 14132 .731 1.367 1.399 1.359 1.388 1.08 52 270 1.384 .99 90 3060 6940 165 174 293 302 0 12581 98 12483 2.158 13105 13007 .463 2.208 1.11 1.143
12 543 483 91 61 452 422 557 494 91 61 466 433 0 0 55 49 10 6 100 100 100 100 874 899 1.071 .934 .929 .934 .927 1.098 52 274 .921 .99 90 3200 6940 165 174 307 316 0 762 96 666 1.474 780 683 .679 1.467 .559 .552
13 3202 5553 91 61 3111 5492 3413 5901 90 61 3322 5840 0 0 547 791 10 6 100 100 100 100 8603 9162 .566 1.765 1.758 1.777 1.739 1.101 52 249 1.753 .99 80 3360 6940 166 174 324 332 0 8764 96 8668 2.786 9314 9217 .359 2.775 1.478 1.472
14 1642 715 90 61 1552 654 1708 729 91 62 1618 668 0 0 283 95 9 6 100 100 100 100 2206 2286 2.373 .421 .413 .427 .414 1.121 52 257 .413 .99 80 3500 6940 166 174 338 346 0 1128 96 1032 .665 1151 1054 1.504 .652 -.588 -.618
15 82 50 90 62 -8 -12 80 47 90 62 -10 -15 0 0 10 10 10 6 3 5 0 0 -20 -25 null null null 1.194 1.25 2.33 52 236 .811 .43 80 3660 6950 167 175 354 362 -50 79 98 -19 null 74 -24 null null null null
16 8057 7738 91 62 7966 7676 9278 8752 91 64 9187 8690 0 0 2734 2237 9 14 100 100 100 100 15642 17877 1.038 .964 .946 1.046 .954 1.333 52 261 .938 .99 80 3800 6930 165 173 368 376 0 12213 98 12115 1.521 13813 13715 .658 1.493 .605 .578
17 2185 770 91 63 2094 707 2254 805 92 63 2163 742 0 0 243 106 13 9 100 100 100 100 2801 2905 2.962 .338 .343 .336 .343 1.084 52 302 .335 .99 90 3960 6930 164 173 383 392 0 1215 99 1116 .533 1271 1171 1.877 .541 -.908 -.885
18 80 50 92 62 -12 -12 79 48 92 62 -13 -14 0 0 9 8 13 6 0 3 0 1 -24 -27 null null null 1.061 .922 2.336 52 216 .469 .36 80 4110 6950 167 175 399 407 -50 79 98 -19 null 76 -22 null null null null
19 10663 5099 91 65 10572 5034 10981 5193 95 67 10890 5128 0 0 1446 748 24 16 100 100 100 100 15606 16018 2.1 .476 .471 .475 .476 1.058 52 306 .469 .99 90 4260 6920 163 172 413 422 0 8048 103 7945 .752 8196 8094 1.331 .743 -.412 -.428
20 12713 19507 95 69 12618 19438 12965 20048 98 75 12870 19979 0 0 1156 2316 25 27 100 100 100 100 32056 32849 .649 1.54 1.552 1.534 1.538 1.063 52 274 1.552 .99 90 4410 6930 164 173 428 437 0 30788 109 30679 2.431 31642 31533 .411 2.45 1.282 1.293

Total number of rows: 44544

Table truncated, full table size 9889 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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