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Sample GSM188467 Query DataSets for GSM188467
Status Public on Jul 19, 2007
Title Basal epidermal cells (Mc1re/Mc1re) -UVB (3) vs. Reference
Sample type RNA
 
Channel 1
Source name Reference (brain, liver, neonate, whole dorsal skin) (20ug)
Organism Mus musculus
Characteristics Reference (brain, liver, neonate, whole dorsal skin) (20ug)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Basal epidermal cells (Mc1re/Mc1re) -UVB (3) (20ug)
Organism Mus musculus
Characteristics Basal epidermal cells (Mc1re/Mc1re) -UVB (3) (20ug)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 7840; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.26; Parameter Scan Time = 13:55:23; Parameter PMT Volts = 570; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 171544; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.26; Parameter Scan Time = 13:55:23; Parameter PMT Volts = 700; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 170541; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.25; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April
Description Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50219.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 May 11, 2007
Last update date Jul 19, 2007
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3119
Series (1)
GSE7778 Basal Epidermis from UVB-irradiated Mc1r and Kit mutants

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
1 461 351 224 284 237 67 499 346 231 312 275 62 0 0 113 128 54 129 92 13 78 1 304 337 3.537 .283 .225 .302 .259 3.733 52 296 10.79 .011 90 1580 8030 14 23 5 14 0 233 189 45 .188 230 41 5.319 .15 -2.411 -2.738
2 1034 1386 202 293 832 1093 1121 1431 210 329 919 1138 0 0 375 552 48 146 98 96 96 90 1925 2057 .761 1.314 1.238 1.292 1.317 1.747 52 300 1.559 .63 90 1730 8030 14 23 20 29 0 922 195 727 .874 952 757 1.145 .823 -.195 -.28
3 443 520 200 289 243 231 458 505 208 319 258 216 0 0 105 130 48 138 92 78 88 22 474 474 1.052 .951 .837 .901 .773 2.169 80 346 6.788 .056 100 1870 8030 14 24 34 44 0 346 192 154 .632 336 144 1.582 .557 -.662 -.845
4 464 615 207 335 257 280 470 433 213 368 263 98 0 0 99 651 48 158 98 28 96 19 537 361 .918 1.089 .373 .55 .374 5.227 52 265 29.328 .011 90 2010 8030 14 23 48 57 0 409 223 186 .725 288 65 1.38 .248 -.465 -2.013
5 547 613 220 436 327 177 578 600 231 457 358 164 0 0 156 143 55 181 92 46 84 5 504 522 1.847 .541 .458 .569 .496 3.346 52 287 1.703 .114 90 2140 8030 14 23 61 70 0 408 290 118 .36 399 109 2.778 .305 -1.474 -1.715
6 651 965 207 380 444 585 663 944 231 666 456 564 0 0 183 295 258 3610 83 0 37 0 1029 1020 .759 1.318 1.237 1.288 1.147 1.987 80 428 1.828 .522 110 2300 8030 13 24 76 87 0 642 253 389 .876 628 375 1.141 .823 -.191 -.282
7 589 616 222 401 367 215 623 586 226 465 401 185 0 0 174 242 48 226 96 40 88 11 582 586 1.707 .586 .461 .514 .453 3.913 52 264 60.878 .001 80 2450 8030 15 23 93 101 0 410 267 143 .39 390 123 2.567 .307 -1.36 -1.705
8 514 580 234 341 280 239 542 566 236 364 308 225 0 0 136 194 58 135 93 75 84 40 519 533 1.172 .854 .731 .769 .738 3.322 32 214 11.355 .033 70 2600 8030 15 22 108 115 0 386 227 159 .568 376 150 1.762 .486 -.817 -1.042
9 1264 3545 223 339 1041 3206 1318 4203 229 383 1095 3864 0 0 672 2119 51 168 93 93 90 87 4247 4959 .325 3.08 3.529 2.865 3.121 1.659 32 226 3.323 .87 70 2740 8020 14 21 122 129 0 2357 225 2132 2.048 2795 2570 .488 2.347 1.034 1.231
10 395 1392 214 323 181 1069 278 1210 220 365 64 887 0 0 231 1300 50 183 53 65 40 62 1250 951 .169 5.906 13.859 5.029 5.268 3.673 32 143 9.702 .334 60 2900 8050 18 24 139 145 0 926 215 711 3.928 805 590 .255 9.217 1.974 3.204
11 421 1037 220 356 201 681 405 1036 229 439 185 680 0 0 142 469 54 406 80 69 69 38 882 865 .295 3.388 3.676 3.369 2.629 2.395 52 268 8.983 .257 80 3040 8030 15 23 152 160 0 690 237 453 2.253 689 452 .444 2.444 1.172 1.289
12 425 1369 222 383 203 986 424 1101 230 484 202 718 0 0 125 928 52 364 84 84 71 46 1189 920 .206 4.857 3.554 4.455 3.11 3.229 32 207 14.541 .164 70 3190 8040 16 23 167 174 0 910 255 656 3.23 732 477 .31 2.364 1.692 1.241
13 359 1084 216 419 143 665 334 819 227 480 118 400 0 0 137 926 50 243 62 59 53 37 808 518 .215 4.65 3.39 3.019 3.029 3.742 32 198 13.085 .177 70 3330 8050 17 24 181 188 0 721 279 442 3.093 545 266 .323 2.254 1.629 1.173
14 469 1225 194 371 275 854 484 1191 195 418 290 820 0 0 117 340 41 230 94 100 92 86 1129 1110 .322 3.105 2.828 3.197 3.127 1.618 52 310 3.856 .657 90 3480 8030 14 23 195 204 0 815 247 568 2.065 792 545 .484 1.88 1.046 .911
15 508 3085 195 380 313 2705 518 2967 194 405 323 2587 0 0 205 1549 32 179 90 98 84 96 3018 2910 .116 8.642 8.009 8.604 8.683 1.798 52 274 9.86 .726 80 3630 8030 15 23 211 219 0 2052 253 1799 5.747 1973 1720 .174 5.326 2.523 2.413
16 273 644 201 420 72 224 225 520 201 465 24 100 0 0 135 428 35 193 46 37 37 18 296 124 .321 3.111 4.167 1.486 1.286 3.335 32 200 10.762 .089 70 3780 8040 16 23 226 233 0 428 279 149 2.069 346 67 .483 2.771 1.049 1.47
17 307 1685 185 407 122 1278 270 1109 189 442 85 702 0 0 139 1635 41 170 62 71 50 59 1400 787 .095 10.475 8.259 7.506 9.018 3.929 32 167 25.604 .186 60 3930 8030 16 22 242 248 0 1121 271 850 6.966 738 467 .144 5.492 2.8 2.457
18 2074 2617 163 310 1911 2307 1184 2239 166 315 1021 1929 0 0 2091 2117 30 96 82 76 80 75 4218 2950 .828 1.207 1.889 1.821 1.246 3.63 52 249 1.109 .673 80 4070 8030 15 23 255 263 0 1740 206 1534 .803 1489 1283 1.246 1.256 -.317 .329
19 279 1210 162 327 117 883 278 537 161 376 116 210 0 0 128 1512 26 242 62 46 56 34 1000 326 .133 7.547 1.81 4.626 10.272 6.419 32 139 32.228 .124 60 4210 8040 17 23 270 276 0 805 217 587 5.019 357 140 .199 1.204 2.327 .268
20 285 973 172 392 113 581 184 761 175 452 12 369 0 0 212 632 31 230 34 56 25 46 694 381 .194 5.142 30.75 7.629 5 3.748 32 193 4.485 .576 70 4360 8040 16 23 284 291 0 647 261 386 3.419 506 245 .292 20.449 1.774 4.354

Total number of rows: 42624

Table truncated, full table size 9240 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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