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Sample GSM156926 Query DataSets for GSM156926
Status Public on Oct 20, 2007
Title ARD075
Sample type RNA
 
Channel 1
Source name mixed reference (FR + CRG)
Organism Homo sapiens
Characteristics mixed reference (FR + CRG)
LabeledExtract: 17463.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name ARD075, 14 days DMEM F12, 15% FCS, Go
Organism Homo sapiens
Characteristics ARD075, 14 days DMEM F12, 15% FCS, Go
LabeledExtract: 17463.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/2001-06/17463.gif
Disease State: CAIS, somatic mosaicism
Cell Line: labia majora
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
1 340 183 217 95 123 88 344 167 222 97 127 72 0 0 70 56 54 31 81 90 59 56 211 199 1.398 .715 .567 .717 .684 2.444 32 138 1.445 .5 60 1530 9190 48 54 50 56 0 195 101 94 .762 178 77 1.313 .604 -.392 -.728
2 248 134 228 105 20 29 228 113 228 108 0 8 0 0 95 78 51 39 25 27 16 17 49 8 .69 1.45 null .651 .67 4.843 120 421 2.109 .39 120 1660 9190 45 57 60 72 -100 143 112 31 1.544 120 9 .648 null .627 null
3 722 372 230 114 492 258 735 356 231 121 505 242 0 0 149 118 51 44 100 98 100 98 750 747 1.907 .524 .479 .495 .505 1.683 52 213 .715 .79 90 1800 9180 45 54 75 84 0 396 121 275 .558 379 258 1.791 .51 -.841 -.971
4 283 135 239 114 44 21 258 114 245 137 19 0 0 0 113 63 69 104 24 13 15 0 65 19 2.095 .477 null .614 .536 3.272 120 443 2.861 .31 120 1940 9190 45 57 88 100 -100 144 121 22 .508 121 0 1.968 null -.976 null
5 728 452 235 100 493 352 729 455 235 107 494 355 0 0 207 103 54 44 93 98 92 98 845 849 1.401 .714 .719 .8 .707 2.364 80 284 .835 .8 100 2080 9190 46 56 103 113 0 481 106 375 .76 485 378 1.315 .765 -.395 -.386
6 252 102 234 90 18 12 231 88 237 96 -3 -2 0 0 90 50 60 35 16 19 10 11 30 -5 1.5 .667 null .702 .71 3.348 120 427 1.195 .46 120 2210 9190 45 57 115 127 -100 109 96 13 .71 94 -2 1.409 null -.494 null
7 724 391 234 88 490 303 759 383 238 91 525 295 0 0 178 101 51 29 98 100 95 98 793 820 1.617 .618 .562 .628 .612 1.79 80 301 .729 .82 100 2350 9190 46 56 130 140 0 416 94 323 .658 408 314 1.519 .598 -.603 -.741
8 710 270 227 88 483 182 746 275 231 91 519 187 0 0 156 79 49 29 100 95 98 93 665 706 2.654 .377 .36 .375 .364 1.81 80 318 .517 .77 100 2490 9180 45 55 144 154 0 288 94 194 .401 293 199 2.492 .384 -1.317 -1.382
9 630 374 226 91 404 283 633 380 227 89 407 289 0 0 189 175 51 27 100 90 96 84 687 696 1.428 .7 .71 .566 .737 2.549 32 144 .951 .78 70 2620 9200 48 55 158 165 0 398 97 301 .746 405 308 1.341 .756 -.423 -.403
10 269 96 238 100 31 -4 258 95 244 104 20 -5 0 0 65 36 58 34 34 9 10 4 27 15 null null null .377 .425 4.887 120 432 19.311 .03 120 2750 9190 45 57 169 181 0 102 106 -4 null 101 -5 null null null null
11 820 162 261 116 559 46 821 144 267 119 560 28 0 0 179 67 57 35 100 46 97 26 605 588 12.152 .082 .05 .089 .097 2.547 80 318 .425 .44 100 2890 9180 45 55 184 194 0 173 124 49 .088 153 30 11.412 .053 -3.512 -4.231
12 390 287 260 123 130 164 387 323 262 129 127 200 0 0 90 95 56 48 78 87 56 75 294 327 .793 1.262 1.575 1.396 1.528 2.238 32 176 2.275 .42 70 3010 9170 45 52 197 204 0 306 131 175 1.343 344 213 .744 1.677 .426 .746
13 386 226 282 145 104 81 382 218 287 149 100 73 0 0 92 63 65 46 65 71 37 37 185 173 1.284 .779 .73 .897 .875 5.16 32 162 2.357 .3 70 3170 9190 47 54 213 220 0 241 154 86 .829 232 78 1.206 .777 -.27 -.363
14 365 201 285 170 80 31 358 202 286 173 73 32 0 0 96 56 61 56 56 34 29 9 111 105 2.581 .388 .438 .553 .58 3.103 120 359 1.993 .33 120 3290 9190 45 57 223 235 -100 214 181 33 .413 215 34 2.423 .467 -1.277 -1.099
15 378 293 304 235 74 58 354 244 312 237 50 9 0 0 185 216 64 74 40 20 15 9 132 59 1.276 .784 .18 .706 .738 3.974 120 278 2.857 .4 120 3420 9190 45 57 236 248 -100 312 250 62 .835 260 10 1.198 .192 -.261 -2.383
16 354 286 335 266 19 20 350 273 340 272 15 7 0 0 75 73 68 60 21 25 7 10 39 22 .95 1.053 .467 .802 .929 4.406 120 311 10.873 .09 120 3560 9190 45 57 250 262 -100 305 283 21 1.121 291 7 .892 .497 .165 -1.009
17 552 481 332 249 220 232 555 471 336 257 223 222 0 0 102 119 70 60 92 94 80 82 452 445 .948 1.055 .996 1.022 .909 2.402 52 192 1.681 .62 90 3690 9170 44 53 264 273 0 512 265 247 1.123 502 236 .891 1.06 .167 .084
18 348 162 328 233 20 -71 339 144 332 235 11 -89 0 0 74 78 70 61 25 5 6 1 -51 -78 null null null 1.906 1.811 3.784 120 335 17.736 .05 120 3830 9190 45 57 277 289 0 173 248 -76 null 153 -95 null null null null
19 339 180 313 187 26 -7 333 168 317 193 20 -19 0 0 70 71 65 60 26 10 6 2 19 1 null null null .778 .734 4.598 120 313 4.393 .21 120 3970 9190 45 57 291 303 0 192 199 -7 null 179 -20 null null null null
20 715 575 292 157 423 418 683 503 299 161 391 346 0 0 287 547 64 45 98 92 98 92 841 737 1.012 .988 .885 .886 .882 1.917 80 248 3.2 .44 100 4100 9170 44 54 305 315 0 612 167 445 1.052 536 368 .95 .942 .074 -.086

Total number of rows: 44544

Table truncated, full table size 9483 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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