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Sample GSM116828 Query DataSets for GSM116828
Status Public on Dec 10, 2007
Title DLA56 PGC1+BRL+RA
Sample type RNA
 
Channel 1
Source name 3 microgrammes amplified RNA from reference pool
Organism Homo sapiens
Characteristics 3 microgrammes amplified RNA from reference pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 3 microgrammes amplified RNA from adipocytes overexpressing PGC1 and treated with BRL+RA
Organism Homo sapiens
Characteristics 3 microgrammes amplified RNA from adipocytes overexpressing PGC1 and treated with BRL+RA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary human tissue, obesity
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49073.gif; format: 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 Jun 28, 2006
Last update date Dec 10, 2007
Contact name Karine Clement
E-mail(s) karine.clement@htd.ap-hop-paris.fr
Phone 33 1 42 34 86 70
Fax 33 1 40 51 00 57
Organization name Hotel-Dieu
Department Service de Medecine et Nutrition
Lab INSERM
Street address place du parvis Notre-Dame
City Paris
ZIP/Postal code U755
Country France
 
Platform ID GPL3942
Series (1)
GSE5184 PGC1alpha overexpression in human white adipose cells

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
1 229 169 101 54 128 115 231 149 102 59 130 95 0 0 64 67 33 36 90 97 81 76 243 225 1.113 .898 .731 .918 .692 2.67 43 178 .846 .53 70 1970 7850 105 112 81 88 0 69 22 47 .366 61 39 2.735 .297 -1.452 -1.75
2 250 208 102 56 148 152 249 195 104 64 147 139 0 0 66 77 32 37 97 93 91 83 300 286 .974 1.027 .946 .977 1.021 1.955 48 242 1.11 .56 80 2110 7860 106 114 95 103 0 93 25 68 .457 87 62 2.187 .421 -1.129 -1.248
3 190 237 96 54 94 183 194 223 101 59 98 169 0 0 69 120 33 34 76 92 65 84 277 267 .514 1.947 1.724 1.366 1.697 4.556 26 156 2.691 .46 60 2250 7850 106 112 110 116 0 137 31 106 1.127 129 98 .888 .998 .172 -.003
4 198 138 101 52 97 86 185 136 103 61 84 84 0 0 43 57 31 35 95 80 80 61 183 168 1.128 .887 1 .776 1.008 2.598 21 169 .887 .46 60 2400 7850 106 112 125 131 0 54 20 34 .349 54 33 2.867 .393 -1.519 -1.346
5 1351 1626 97 58 1254 1568 1347 1708 105 64 1250 1650 0 0 548 620 85 34 97 100 89 100 2822 2900 .8 1.25 1.32 1.364 1.248 2.54 47 276 1.24 .89 80 2550 7850 105 113 139 147 0 1654 59 1595 1.272 1737 1678 .786 1.343 .347 .425
6 254 156 96 57 158 99 248 137 98 63 152 80 0 0 53 68 31 36 97 81 94 56 257 232 1.596 .627 .526 .57 .513 2.906 37 148 .596 .52 60 2700 7850 106 112 155 161 0 54 20 35 .218 48 28 4.58 .183 -2.195 -2.447
7 540 526 90 58 450 468 468 477 93 64 378 419 0 0 302 253 30 35 95 100 95 100 918 797 .962 1.04 1.108 1.169 .981 2.465 46 254 .956 .82 80 2840 7850 105 113 168 176 0 321 35 285 .634 291 256 1.577 .676 -.657 -.565
8 413 407 91 58 322 349 405 388 96 65 314 330 0 0 122 140 34 39 100 98 98 98 671 644 .923 1.084 1.051 1.128 1.141 1.671 56 289 1.098 .84 90 2990 7850 104 113 182 191 0 226 32 194 .602 215 183 1.662 .583 -.733 -.777
9 328 394 91 59 237 335 324 397 98 74 233 338 0 0 77 114 35 66 100 98 100 98 572 571 .707 1.414 1.451 1.45 1.372 1.609 55 271 1.572 .8 90 3150 7860 105 114 198 207 0 234 35 199 .839 236 201 1.192 .861 -.253 -.216
10 623 516 84 60 539 456 635 543 92 76 551 483 0 0 198 190 33 75 100 97 100 95 995 1034 1.182 .846 .877 .819 .862 1.646 43 159 .852 .91 70 3280 7850 105 112 212 219 0 296 34 261 .485 311 277 2.063 .502 -1.045 -.993
11 1169 1341 92 55 1077 1286 1271 1359 95 65 1179 1304 0 0 349 328 33 44 98 100 98 100 2363 2483 .837 1.194 1.106 1.205 1.181 1.497 64 276 1.164 .92 90 3430 7850 104 113 226 235 0 1267 52 1215 1.128 1284 1232 .887 1.045 .174 .063
12 1552 1840 99 57 1453 1783 1455 1699 101 84 1356 1642 0 0 623 827 33 94 97 100 97 100 3236 2998 .815 1.227 1.211 1.311 1.16 2.283 48 156 1.255 .93 70 3570 7850 105 112 241 248 0 1910 59 1851 1.274 1764 1705 .785 1.257 .349 .33
13 2237 3140 97 61 2140 3079 2463 3429 98 87 2366 3368 0 0 795 1005 32 98 98 98 98 98 5219 5734 .695 1.439 1.423 1.419 1.438 2.234 55 233 1.445 .93 80 3720 7850 105 113 256 264 0 3609 70 3539 1.654 3941 3871 .605 1.636 .726 .71
14 1077 947 95 62 982 885 1131 961 99 76 1036 899 0 0 302 273 37 74 100 100 100 99 1867 1935 1.11 .901 .868 .898 .894 1.329 100 403 .888 .96 110 3870 7850 103 114 269 280 0 717 47 670 .683 728 681 1.465 .657 -.551 -.605
15 136 73 97 61 39 12 127 67 102 73 30 6 0 0 59 36 36 52 43 9 21 3 51 36 3.25 .308 .2 .366 .361 6.06 32 185 10.396 .05 70 4010 7850 105 112 285 292 -50 17 14 3 .071 16 1 14.037 .046 -3.811 -4.433
16 2799 3069 102 60 2697 3009 2885 3029 102 71 2783 2969 0 0 1136 1179 32 52 100 100 98 100 5706 5752 .896 1.116 1.067 1.199 1.077 2.23 54 264 1.103 .94 80 4160 7850 105 113 300 308 0 3146 62 3084 1.144 3105 3043 .874 1.094 .194 .129
17 7546 9083 96 63 7450 9020 6194 8372 101 80 6098 8309 0 0 3632 3626 33 81 98 100 98 100 16470 14407 .826 1.211 1.363 1.305 1.224 1.941 69 283 1.133 .93 90 4310 7840 103 112 314 323 0 9222 64 9158 1.229 8500 8436 .813 1.383 .298 .468
18 110 70 98 58 12 12 105 61 104 71 7 3 0 0 41 39 36 48 15 15 12 6 24 10 1 1 .429 .784 1.01 5.222 32 203 -1 -1 70 4450 7850 105 112 329 336 -50 27 22 5 .385 23 1 2.599 .165 -1.378 -2.6
19 2961 4147 95 59 2866 4088 3002 4307 100 72 2907 4248 0 0 1006 1356 37 50 100 100 100 100 6954 7155 .701 1.426 1.461 1.451 1.411 1.824 66 293 1.465 .9 90 4600 7850 104 113 343 352 0 4695 67 4628 1.615 4876 4809 .619 1.654 .691 .726
20 1874 1449 102 61 1772 1388 1989 1540 106 70 1887 1479 0 0 606 464 33 44 100 100 100 100 3160 3366 1.277 .783 .784 .789 .762 1.695 55 211 .763 .93 80 4750 7850 105 113 359 367 0 1228 52 1176 .664 1305 1253 1.507 .664 -.592 -.591

Total number of rows: 43104

Table truncated, full table size 9724 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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