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Sample GSM466848 Query DataSets for GSM466848
Status Public on Nov 10, 2009
Title mock 12 hrs.C-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: mock 12 hrs.C-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/2008-07/80428.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 1174 820 51 344 1123 476 1228 813 51 365 1177 469 0 0 177 164 5 143 100 98 100 90 1599 1646 2.359 .424 .398 .401 .4 1.495 52 258 .4 .76 80 1620 7040 209 217 136 144 0 2288 960 1328 1.183 2268 1309 .846 1.112 .242 .153
2 1265 893 53 500 1212 393 1315 900 54 534 1262 400 0 0 155 179 6 194 100 88 100 51 1605 1662 3.084 .324 .317 .287 .352 1.761 52 216 .358 .64 90 1770 7040 208 217 150 159 0 2491 1395 1096 .905 2511 1116 1.105 .884 -.145 -.177
3 19973 14408 56 674 19917 13734 29093 19691 89 734 29037 19017 0 0 13189 9111 116 273 92 90 87 86 33651 48054 1.45 .69 .655 .838 .701 1.783 80 270 .7 .98 100 1920 7030 207 217 165 175 100 40199 1880 38318 1.924 54938 53058 .52 1.827 .944 .87
4 940 975 60 771 880 204 1209 945 91 818 1149 174 0 0 425 261 116 259 88 31 85 13 1084 1323 4.314 .232 .151 .351 .283 3.658 80 270 .209 .23 100 2070 7030 207 217 180 190 100 2720 2151 569 .647 2637 485 1.546 .423 -.629 -1.243
5 2603 519 59 800 2544 -281 2684 510 60 814 2625 -290 0 0 230 148 8 224 100 0 100 0 2263 2335 null null null .036 .051 4.294 52 171 -.12 -.54 80 2220 7040 209 217 196 204 0 1448 2232 -784 -.308 1423 -809 -3.245 -.308 null null
6 11605 10055 60 876 11545 9179 14348 12306 107 909 14288 11430 0 0 6269 4350 223 344 98 100 96 100 20724 25718 1.258 .795 .8 .915 .778 1.71 120 368 .754 .98 120 2380 7040 207 219 210 222 0 28054 2444 25610 2.218 34334 31890 .451 2.232 1.149 1.158
7 607 906 64 959 543 -53 316 438 139 1015 252 -521 0 0 1068 1215 276 367 30 16 13 10 490 -269 null null null 2.263 .988 9.445 80 247 1.163 .84 100 2530 7040 208 218 226 236 -100 2528 2676 -148 -.272 1222 -1454 -3.672 -5.768 null null
8 28807 20921 68 1031 28739 19890 30078 21534 81 1054 30010 20503 0 0 5899 3594 81 259 100 100 100 100 48629 50513 1.445 .692 .683 .704 .69 1.134 52 198 .678 .99 90 2680 7040 208 217 241 250 0 58370 2877 55494 1.931 60080 57204 .518 1.906 .949 .931
9 62 504 67 1081 -5 -577 60 325 70 1110 -7 -756 0 0 8 426 34 296 0 5 0 0 -582 -763 null null null 79.745 85.909 2.156 80 260 73.33 .27 100 2820 7030 207 217 255 265 -50 1406 3016 -1610 321.969 907 -2109 .003 301.323 8.331 8.235
10 88 617 67 1121 21 -504 89 390 71 1141 22 -731 0 0 10 529 33 304 2 11 0 1 -483 -709 null null null 25.913 31.639 2.622 80 287 -86.356 -.47 100 2970 7030 207 217 270 280 -50 1721 3128 -1406 -66.961 1088 -2040 -.015 -92.705 null null
11 6874 6759 66 1107 6808 5652 7070 7031 72 1126 7004 5924 0 0 740 1033 18 268 100 100 100 100 12460 12928 1.205 .83 .846 .815 .842 1.177 52 203 .853 .97 80 3130 7030 208 216 287 295 0 18858 3089 15769 2.316 19617 16528 .432 2.36 1.212 1.239
12 264 469 64 974 200 -505 326 254 66 997 262 -720 0 0 112 421 19 224 86 7 80 2 -305 -458 null null null 12.071 8.243 2.759 80 284 -4.198 -.81 100 3280 7030 207 217 301 311 100 1309 2717 -1409 -7.045 709 -2009 -.142 -7.667 null null
13 4870 1972 63 947 4807 1025 5107 1988 64 989 5044 1041 0 0 836 296 8 265 100 100 100 92 5832 6085 4.69 .213 .206 .206 .205 1.387 52 193 .204 .85 80 3430 7030 208 216 317 325 0 5502 2642 2860 .595 5547 2904 1.681 .576 -.749 -.796
14 409 574 63 1003 346 -429 507 431 63 999 444 -572 0 0 175 326 7 236 90 5 87 2 -83 -128 null null null 5.6 11.857 12.781 80 268 -2.203 -.69 100 3580 7030 207 217 331 341 100 1601 2798 -1197 -3.459 1203 -1596 -.289 -3.594 null null
15 50 392 64 982 -14 -590 47 197 65 1021 -17 -785 0 0 10 335 7 273 2 0 1 0 -604 -802 null null null 38.442 41.157 1.958 80 270 54.298 .71 100 3730 7030 207 217 346 356 -50 1094 2740 -1646 117.58 550 -2190 .009 128.834 6.877 7.009
16 8026 1486 65 1066 7961 420 8237 1447 66 1093 8172 381 0 0 894 216 6 299 100 69 100 21 8381 8553 18.955 .053 .047 .044 .054 1.94 52 193 .052 .53 80 3880 7030 208 216 362 370 0 4146 2974 1172 .147 4037 1063 6.794 .13 -2.764 -2.943
17 353 523 65 1014 288 -491 435 277 65 1093 370 -737 0 0 147 500 6 331 92 10 91 3 -203 -367 null null null 4.016 6.13 4.078 80 269 -3.63 -.76 100 4030 7030 207 217 376 386 100 1459 2829 -1370 -4.757 773 -2056 -.21 -5.557 null null
18 52 462 65 1019 -13 -557 48 237 66 1063 -17 -782 0 0 12 412 8 259 7 2 2 0 -570 -799 null null null 36.908 39.271 2.163 80 278 53.442 .56 100 4180 7020 206 216 391 401 -50 1289 2843 -1554 119.542 661 -2182 .008 128.341 6.901 7.004
19 1942 2778 67 1061 1875 1717 2080 2756 111 1111 2013 1695 0 0 417 379 471 356 98 100 95 97 3592 3708 1.092 .916 .842 .924 .889 1.264 80 286 .929 .92 100 4330 7030 207 217 406 416 0 7751 2960 4790 2.555 7689 4729 .391 2.349 1.353 1.232
20 15983 7357 68 1123 15915 6234 16319 7352 122 1136 16251 6229 0 0 1635 741 519 355 100 100 100 100 22149 22480 2.553 .392 .383 .392 .389 1.12 52 235 .386 .97 90 4490 7030 207 216 422 431 0 20526 3133 17393 1.093 20512 17379 .915 1.069 .128 .097

Total number of rows: 44544

Table truncated, full table size 10460 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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