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Sample GSM188473 Query DataSets for GSM188473
Status Public on Jul 19, 2007
Title Basal epidermal cells (+/+) -UVB (1) 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 (+/+) -UVB (1) (20ug)
Organism Mus musculus
Characteristics Basal epidermal cells (+/+) -UVB (1) (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 = 1360, 8120; 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 = 39.22; Parameter Scan Time = 12:35:35; Parameter PMT Volts = 530; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 171465; 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 = 39.22; Parameter Scan Time = 12:35:35; Parameter PMT Volts = 750; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 170462; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.23; 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/2004-03/50213.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
1 687 600 155 287 532 313 728 614 157 300 573 327 0 0 242 189 30 97 100 86 98 69 845 900 1.7 .588 .571 .608 .602 1.78 52 326 .656 .593 90 1490 8260 9 18 8 17 0 429 205 224 .421 439 234 2.377 .408 -1.249 -1.293
2 1524 2289 159 301 1365 1988 1548 2354 278 577 1389 2053 0 0 511 943 961 1950 75 57 19 0 3353 3442 .687 1.456 1.478 1.368 1.427 1.281 52 285 1.596 .917 90 1640 8270 10 19 23 32 0 1636 215 1421 1.041 1683 1468 .96 1.057 .058 .08
3 768 829 156 274 612 555 853 849 153 280 697 575 0 0 369 340 36 77 95 92 90 88 1167 1272 1.103 .907 .825 .977 .955 1.612 80 378 4.199 .265 100 1780 8260 9 19 37 47 0 593 196 397 .648 607 411 1.542 .59 -.625 -.762
4 776 626 158 261 618 365 793 611 162 267 635 350 0 0 156 150 20 72 100 100 100 96 983 985 1.693 .591 .551 .562 .53 1.497 52 265 .619 .649 90 1930 8270 10 19 52 61 0 448 187 261 .422 437 250 2.368 .394 -1.244 -1.344
5 849 1427 158 274 691 1153 952 1037 154 292 794 763 0 0 399 2929 37 99 97 100 92 91 1844 1557 .599 1.669 .961 1.329 1.097 1.891 80 373 8.018 .277 100 2070 8260 9 19 66 76 0 1020 196 824 1.193 741 545 .838 .687 .254 -.542
6 871 1751 156 261 715 1490 925 1683 151 279 769 1422 0 0 397 1054 40 99 99 100 95 99 2205 2191 .48 2.084 1.849 2.12 2.012 1.868 120 544 2.373 .863 130 2230 8260 7 20 80 93 0 1252 187 1065 1.49 1203 1017 .671 1.322 .575 .403
7 919 954 158 247 761 707 1030 978 158 273 872 731 0 0 388 335 24 109 100 100 96 92 1468 1603 1.076 .929 .838 1.071 .92 1.918 52 250 .922 .781 80 2370 8260 10 18 97 105 0 682 177 505 .664 699 523 1.506 .599 -.59 -.739
8 847 1013 169 258 678 755 878 978 169 273 709 720 0 0 221 406 23 90 100 93 100 87 1433 1429 .898 1.114 1.016 .93 1.085 1.758 32 220 1.252 .878 70 2510 8260 10 17 111 118 0 724 184 540 .796 699 515 1.256 .726 -.329 -.462
9 1579 6763 166 242 1413 6521 1146 7074 169 261 980 6832 0 0 1017 4983 23 94 100 100 100 96 7934 7812 .217 4.615 6.971 3.846 4.278 1.754 32 231 4.894 .942 70 2660 8260 10 17 126 133 0 4835 173 4662 3.299 5057 4884 .303 4.984 1.722 2.317
10 299 1146 161 225 138 921 201 588 163 228 40 363 0 0 227 1161 23 65 62 68 46 56 1059 403 .15 6.674 9.075 5.948 6 3.277 32 164 7.117 .569 60 2820 8270 12 18 143 149 0 819 161 658 4.771 420 260 .21 6.488 2.254 2.698
11 635 1194 181 230 454 964 623 1259 183 257 442 1029 0 0 280 623 25 92 100 87 100 84 1418 1471 .471 2.123 2.328 2.089 2.09 2.028 32 160 2.394 .785 60 2960 8270 12 18 157 163 0 854 164 689 1.518 900 736 .659 1.664 .602 .735
12 344 474 173 228 171 246 246 268 177 245 73 40 0 0 212 404 25 85 80 46 69 38 417 113 .695 1.439 .548 1.943 1.348 3.381 52 329 2.339 .431 90 3100 8260 9 18 169 178 0 339 163 176 1.028 192 29 .972 .392 .041 -1.352
13 215 197 180 223 35 -26 176 170 183 252 -4 -53 0 0 92 83 33 121 28 9 25 0 9 -57 null null null 1.696 2.078 5.806 52 302 6.991 .057 90 3250 8260 9 18 184 193 0 141 159 -19 null 122 -38 null null null null
14 822 1194 189 258 633 936 908 1221 192 292 719 963 0 0 220 529 36 142 100 90 100 86 1569 1682 .676 1.479 1.339 1.287 1.416 1.646 52 264 1.732 .841 80 3390 8260 10 18 199 207 0 854 184 669 1.057 873 688 .946 .958 .08 -.063
15 651 5310 187 243 464 5067 613 3477 190 264 426 3234 0 0 370 4987 25 97 100 84 94 84 5531 3660 .092 10.92 7.592 7.061 9.023 2.733 52 271 12.702 .933 80 3550 8260 10 18 215 223 0 3796 174 3622 7.807 2486 2312 .128 5.427 2.965 2.44
16 514 609 186 259 328 350 438 465 187 272 252 206 0 0 243 439 26 93 96 59 93 50 678 458 .937 1.067 .817 .996 1.194 2.279 32 211 1.619 .712 70 3700 8260 10 17 230 237 0 435 185 250 .763 332 147 1.311 .584 -.39 -.775
17 301 804 178 231 123 573 227 799 177 246 49 568 0 0 159 486 24 100 62 75 50 68 696 617 .215 4.659 11.592 6.839 7.171 3.185 32 151 5.485 .422 60 3850 8270 12 18 246 252 0 575 165 410 3.33 571 406 .3 8.287 1.736 3.051
18 2354 5086 165 220 2189 4866 1054 2513 166 227 889 2293 0 0 2667 5517 22 77 98 92 98 84 7055 3182 .45 2.223 2.579 2.334 2.182 2.054 52 226 2.154 .953 80 3990 8270 11 19 259 267 0 3636 157 3479 1.589 1797 1639 .629 1.844 .668 .883
19 289 920 168 219 121 701 238 784 168 229 70 565 0 0 137 816 22 85 71 65 59 62 822 635 .173 5.793 8.071 4.586 5.667 4.103 32 143 10.286 .329 60 4120 8270 12 18 273 279 0 658 157 501 4.142 560 404 .241 5.77 2.05 2.529
20 516 1256 177 251 339 1005 372 907 180 280 195 656 0 0 323 1020 26 122 100 71 96 65 1344 851 .337 2.965 3.364 1.789 2.629 4.179 32 167 3.414 .822 60 4280 8270 12 18 289 295 0 898 179 718 2.119 648 469 .472 2.405 1.084 1.266

Total number of rows: 42624

Table truncated, full table size 9371 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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