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Sample GSM156938 Query DataSets for GSM156938
Status Public on Oct 20, 2007
Title ARD407
Sample type RNA
 
Channel 1
Source name mixed reference (FR + CRG)
Organism Homo sapiens
Characteristics mixed reference (FR + CRG)
LabeledExtract: 17430.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name ARD407, 14 days DMEM F12, 15% FCS, G0
Organism Homo sapiens
Characteristics ARD407, 14 days DMEM F12, 15% FCS, G0
LabeledExtract: 17430.Channel_2
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17430.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY
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 Jan 18, 2007
Last update date Oct 20, 2007
Contact name Paul-Martin Holterhus
E-mail(s) holterhus@pediatrics.uni-kiel.de
Phone +49 (0) 431-597 3959
Fax +49 (0) 431-597 3966
Organization name Universitätsklinikum Schleswig-Holstein
Department Pädiatrische Endokrinologie und Diabetologie
Lab Klinik für Allgemeine Pädiatrie
Street address Campus Kiel, Schwanenweg 20
City Kiel
ZIP/Postal code D-24105
Country Germany
 
Platform ID GPL3039
Series (1)
GSE6796 Fibroblasts from genital and extragenital regions of 46,XY individuals

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
1 445 321 196 103 249 218 436 289 234 111 240 186 0 0 152 151 360 104 18 76 0 45 467 426 1.142 .876 .775 .824 .851 1.956 80 450 .757 .6 110 2020 9280 50 61 56 67 -100 361 116 245 .986 325 209 1.015 .872 -.021 -.197
2 715 523 204 113 511 410 777 590 209 119 573 477 0 0 239 166 62 42 96 96 90 90 921 1050 1.246 .802 .832 .807 .767 1.448 32 136 .896 .88 70 2180 9290 53 60 74 81 0 589 127 462 .903 664 537 1.107 .937 -.147 -.094
3 1850 1070 208 112 1642 958 1867 1097 211 117 1659 985 0 0 399 284 53 39 100 100 100 98 2600 2644 1.714 .583 .594 .57 .564 1.296 80 268 .638 .93 100 2300 9280 51 61 85 95 0 1205 126 1078 .657 1235 1109 1.523 .668 -.606 -.581
4 224 149 202 108 22 41 214 129 208 112 12 21 0 0 56 85 51 33 23 38 6 17 63 33 .537 1.864 1.75 1.168 1.313 4.591 80 225 3.395 .32 100 2430 9280 51 61 98 108 0 168 122 46 2.098 145 24 .477 1.97 1.069 .978
5 1116 1046 201 112 915 934 1115 941 204 113 914 829 0 0 242 309 50 29 100 100 100 100 1849 1743 .98 1.021 .907 1.014 1.007 1.319 80 281 1.126 .92 100 2550 9260 49 59 110 120 0 1178 126 1051 1.149 1059 933 .87 1.021 .201 .03
6 553 423 192 118 361 305 520 400 199 119 328 282 0 0 281 282 50 30 87 71 71 68 666 610 1.184 .845 .86 .805 .83 2.02 32 115 1.113 .81 60 2690 9270 52 58 126 132 0 476 133 343 .951 450 317 1.051 .968 -.072 -.047
7 992 1043 191 126 801 917 1011 992 198 127 820 866 0 0 285 327 48 27 100 100 100 100 1718 1686 .874 1.145 1.056 1.155 1.149 1.273 80 337 1.224 .92 110 2820 9260 48 59 136 147 0 1174 142 1032 1.289 1117 975 .776 1.189 .366 .25
8 1321 1453 190 128 1131 1325 1324 1402 196 130 1134 1274 0 0 268 315 47 29 100 100 100 100 2456 2408 .854 1.172 1.123 1.174 1.192 1.258 80 242 1.245 .94 100 2960 9260 49 59 151 161 0 1636 144 1492 1.319 1578 1434 .758 1.265 .399 .339
9 1237 877 203 138 1034 739 1225 940 209 147 1022 802 0 0 414 343 70 64 100 98 100 93 1773 1824 1.399 .715 .785 .67 .716 1.627 80 277 .804 .92 100 3080 9260 49 59 163 173 0 987 155 832 .805 1058 903 1.243 .883 -.314 -.179
10 404 280 221 149 183 131 412 275 251 199 191 126 0 0 73 81 120 167 81 15 12 3 314 317 1.397 .716 .66 .636 .641 2.382 32 165 1.984 .74 70 3220 9270 51 58 178 185 0 315 168 147 .806 310 142 1.241 .743 -.311 -.429
11 1236 283 205 140 1031 143 1253 240 223 166 1048 100 0 0 268 146 88 120 98 42 98 20 1174 1148 7.21 .139 .095 .11 .114 2.253 80 368 .455 .55 110 3370 9250 47 58 191 202 0 319 158 161 .156 270 113 6.405 .107 -2.679 -3.219
12 858 953 209 152 649 801 840 959 215 162 631 807 0 0 185 163 50 57 100 100 100 100 1450 1438 .81 1.234 1.279 1.263 1.244 1.403 80 220 1.308 .92 100 3500 9260 49 59 205 215 0 1073 171 902 1.389 1080 908 .72 1.44 .474 .526
13 443 353 210 146 233 207 430 326 218 157 220 180 0 0 214 224 54 64 67 70 61 59 440 400 1.126 .888 .818 .815 .849 2.391 120 357 1.291 .74 120 3620 9260 48 60 216 228 -100 397 164 233 1 367 203 1 .921 0 -.119
14 649 370 203 128 446 242 652 349 211 141 449 221 0 0 172 127 56 53 100 98 100 88 688 670 1.843 .543 .492 .511 .534 1.631 52 196 .731 .83 80 3760 9250 49 57 232 240 -100 417 144 272 .611 393 249 1.637 .554 -.711 -.852
15 636 451 198 119 438 332 636 438 202 132 438 319 0 0 193 149 54 128 100 97 97 58 770 757 1.319 .758 .728 .765 .79 1.616 80 272 .913 .85 100 3900 9260 49 59 245 255 0 508 134 374 .853 493 359 1.172 .82 -.229 -.287
16 1327 887 203 131 1124 756 1189 824 203 134 986 693 0 0 766 350 47 39 100 100 100 98 1880 1679 1.487 .673 .703 .663 .718 1.559 80 281 .739 .8 100 4030 9250 48 58 258 268 0 999 147 851 .757 928 780 1.321 .791 -.401 -.338
17 696 689 200 129 496 560 715 591 204 146 515 462 0 0 222 332 52 160 100 100 100 83 1056 977 .886 1.129 .897 1.093 1.032 1.522 80 303 1.413 .84 110 4170 9260 48 59 271 282 0 776 145 630 1.271 665 520 .787 1.01 .346 .014
18 507 1244 196 121 311 1123 482 1143 199 123 286 1022 0 0 140 327 50 29 97 100 95 100 1434 1308 .277 3.611 3.573 3.804 3.592 1.513 80 275 3.694 .85 110 4310 9260 48 59 285 296 0 1400 136 1264 4.065 1287 1150 .246 4.023 2.023 2.008
19 509 375 197 116 312 259 511 309 205 120 314 193 0 0 110 149 52 31 100 100 98 98 571 507 1.205 .83 .615 .761 .797 1.691 80 248 1.322 .75 100 4440 9250 48 58 299 309 0 422 131 292 .935 348 217 1.07 .692 -.098 -.531
20 1062 1003 209 114 853 889 1058 968 210 119 849 854 0 0 191 227 53 33 100 100 100 100 1742 1703 .96 1.042 1.006 1.034 1.025 1.313 80 254 1.13 .91 100 4570 9250 48 58 312 322 0 1129 128 1001 1.173 1090 961 .852 1.132 .231 .179

Total number of rows: 44544

Table truncated, full table size 9398 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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