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Sample GSM466837 Query DataSets for GSM466837
Status Public on Nov 10, 2009
Title mir-124 12 hrs IP #2 (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 IP #2 (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/2008-07/80606.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 1267 818 38 62 1229 756 1299 819 38 65 1261 757 0 0 161 101 3 14 100 100 100 100 1985 2018 1.626 .615 .6 .616 .609 1.09 52 284 .601 .99 80 1680 6670 139 147 156 164 0 1277 97 1180 .96 1278 1182 1.041 .937 -.059 -.094
2 1423 902 38 64 1385 838 1443 923 41 68 1405 859 0 0 143 87 15 21 100 100 100 100 2223 2264 1.653 .605 .611 .605 .609 1.091 52 295 .592 .98 90 1820 6670 138 147 169 178 0 1408 100 1308 .944 1441 1341 1.059 .954 -.082 -.067
3 13893 7588 39 66 13854 7522 14360 7754 41 71 14321 7688 0 0 2566 1084 15 23 100 100 100 100 21376 22009 1.842 .543 .537 .555 .54 1.156 52 302 .528 .99 90 1980 6670 138 147 185 194 0 11845 103 11742 .848 12104 12001 1.18 .838 -.239 -.255
4 1397 986 39 66 1358 920 1432 993 39 68 1393 927 0 0 261 132 3 15 100 100 100 100 2278 2320 1.476 .677 .665 .689 .669 1.165 52 245 .644 .99 80 2130 6670 139 147 201 209 0 1539 103 1436 1.058 1550 1447 .946 1.039 .081 .055
5 1853 1035 39 65 1814 970 1897 1068 39 67 1858 1003 0 0 281 203 2 15 100 100 100 100 2784 2861 1.87 .535 .54 .526 .538 1.122 52 217 .534 .99 80 2270 6670 139 147 215 223 0 1616 101 1514 .835 1667 1566 1.198 .843 -.261 -.247
6 12008 8781 39 63 11969 8718 13240 9576 43 67 13201 9513 0 0 3442 2170 64 24 100 100 100 100 20687 22714 1.373 .728 .721 .761 .722 1.257 80 373 .705 .99 110 2420 6660 136 147 228 239 0 13707 98 13609 1.137 14948 14850 .88 1.125 .185 .17
7 186 113 39 69 147 44 190 111 46 73 151 42 0 0 30 23 81 28 94 78 25 23 191 193 3.341 .299 .278 .28 .282 1.628 52 231 .27 .58 80 2570 6680 140 148 245 253 0 176 108 69 .467 173 66 2.14 .434 -1.098 -1.204
8 12329 6858 39 67 12290 6791 14701 8062 40 69 14662 7995 0 0 5424 2751 6 15 100 100 100 100 19081 22657 1.81 .553 .545 .606 .553 1.366 80 338 .535 .99 100 2730 6660 137 147 260 270 0 10705 105 10601 .863 12585 12480 1.159 .851 -.213 -.232
9 39 58 39 65 0 -7 39 44 39 67 0 -21 0 0 3 30 3 13 17 25 1 17 -7 -21 null null null 11.234 12 1.867 52 238 25.426 .26 80 2880 6660 138 146 276 284 -50 91 101 -11 null 69 -33 0 null null null
10 55 58 39 63 16 -5 55 54 39 65 16 -9 0 0 6 19 3 14 98 11 94 5 11 7 null null null 1.332 2.6 6.589 52 243 -8.985 -.23 80 3030 6660 138 146 291 299 -50 91 98 -8 -.488 84 -14 -2.05 -.878 null null
11 3737 4551 39 66 3698 4485 3867 4669 40 69 3828 4603 0 0 613 624 19 21 100 100 100 100 8183 8431 .825 1.213 1.202 1.228 1.212 1.128 52 273 1.194 .99 90 3170 6670 138 147 304 313 0 7104 103 7001 1.893 7288 7185 .528 1.877 .921 .908
12 172 90 39 66 133 24 172 89 40 68 133 23 0 0 12 15 19 20 100 55 100 11 157 156 5.542 .18 .173 .158 .175 1.945 52 276 .155 .41 90 3330 6670 138 147 320 329 0 140 103 37 .282 139 36 3.55 .27 -1.828 -1.889
13 2668 3109 39 68 2629 3041 2788 3272 39 69 2749 3204 0 0 513 708 3 14 100 100 100 100 5670 5953 .865 1.157 1.166 1.137 1.177 1.142 52 264 1.166 .99 80 3480 6660 138 146 336 344 0 4853 106 4747 1.806 5108 5001 .554 1.819 .853 .863
14 250 1110 39 69 211 1041 260 1150 39 72 221 1081 0 0 40 212 3 16 100 100 100 100 1252 1302 .203 4.934 4.891 4.89 4.982 1.134 52 293 5.033 .98 90 3650 6660 137 146 352 361 0 1733 108 1625 7.701 1795 1687 .13 7.636 2.945 2.933
15 37 53 39 67 -2 -14 37 41 39 71 -2 -26 0 0 4 22 3 17 3 15 1 1 -16 -28 null null null 6.719 6.533 2.31 52 235 16.543 .46 80 3790 6650 137 145 367 375 -50 83 105 -22 10.927 64 -41 .092 20.293 3.45 4.343
16 4485 1493 39 71 4446 1422 4509 1555 40 73 4470 1484 0 0 500 263 3 16 100 100 100 100 5868 5954 3.127 .32 .332 .315 .328 1.154 52 227 .32 .99 80 3930 6660 138 146 381 389 0 2331 111 2220 .499 2427 2317 2.003 .518 -1.002 -.948
17 87 137 39 69 48 68 91 137 39 72 52 68 0 0 20 26 3 15 93 98 93 93 116 120 .706 1.417 1.308 1.606 1.336 2.281 80 350 1.566 .77 100 4080 6660 137 147 395 405 0 214 108 106 2.211 214 106 .452 2.041 1.145 1.029
18 37 56 39 68 -2 -12 37 42 39 73 -2 -26 0 0 3 30 3 19 3 15 0 11 -14 -28 null null null 8.274 7.5 2.131 52 258 14.68 .41 80 4240 6650 137 145 412 420 -50 87 106 -19 9.366 66 -41 .107 20.293 3.227 4.343
19 2165 15068 40 72 2125 14996 2211 15381 41 77 2171 15309 0 0 261 1287 9 28 100 100 100 100 17121 17480 .142 7.057 7.052 7.094 6.996 1.066 52 287 6.863 .99 90 4380 6660 137 146 425 434 0 23521 112 23409 11.016 24010 23897 .091 11.008 3.462 3.46
20 8443 4147 40 70 8403 4077 9761 4733 41 74 9721 4663 0 0 3407 1532 8 24 100 98 100 98 12480 14384 2.061 .485 .48 .551 .483 1.505 80 321 .467 .99 100 4540 6660 137 147 441 451 0 6473 109 6364 .757 7388 7279 1.32 .749 -.401 -.417

Total number of rows: 44544

Table truncated, full table size 9350 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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