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Sample GSM799003 Query DataSets for GSM799003
Status Public on Jan 12, 2012
Title P66
Sample type RNA
 
Channel 1
Source name Stratagene Universal Human Reference
Organism Homo sapiens
Characteristics reference: Stratagene Universal Human Reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name C
Organism Homo sapiens
Characteristics tissue: skin
age: 35 years
organism part: chest
disease state: inactive
individual: 66
Sex: M
Extracted molecule total RNA
Extraction protocol Poly-adenylated RNA was extracted from snap-frozen skin biopsy specimens (DM and lupus) using a two step method. First, total RNA was extracted with phenol-guanidine thiocyaniate extraction (RNAbee ,Tel-Test, Friendswood TX). Next, poly-adenylated RNA was purified using RNeasy Kit (Quiagen, Chatsworth, CA) according to the manufacturers instructions. Sample RNA and reference mRNA (Stratagene) were amplified using an Amino Allyl MessageAmp II aRNA kit (Ambion, Austin, TX).
Label Cy5
Label protocol not provided
 
 
Hybridization protocol (labeled with Cy5) and amplified Human Universal Reference RNA (labeled with Cy3) (Stratagene, La Jolla, CA) were competitively hybridized to HEEBO (human exon evidence-based oligonucleotide) microarrays as described (http://www.microarray.org/sfgf/heebo.do).
Scan protocol GenePix 4000A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68140.gif
Data processing Array data were filtered based on fluorescent hybridization signal 1.5-fold over local background in either the Cy5 or the Cy3 channel and if the data were technically adequate in 80% of experiments. Array data underwent LOWESS normalization, and the data were displayed as a log2 ratio of LOWESS-normalized Cy5/Cy3 ratio (span parameter=0.4)
 
Submission date Sep 20, 2011
Last update date Jan 12, 2012
Contact name David Fiorentino
E-mail(s) fiorentino@stanford.edu
Phone 650-498-6120
Fax 650-723-7796
Organization name Stanford University
Department Dermatology
Lab Blake Wilbur Clinic, W0074
Street address 900 Blake Wilbur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL9258
Series (1)
GSE32245 Fiorentino 2006-7 dermatomyositis, lupus, control skin

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 21051 8799 197 270 20854 8529 24157 10295 197 272 23960 10025 0 0 8534 3492 32 35 100 100 100 100 29383 33985 2.445 .409 .418 .411 .406 1.417 80 480 .405 .99 110 1960 5750 61 72 58 69 0 11107 341 10766 .516 12995 12654 1.937 .528 -.954 -.921
2 21850 9410 196 271 21654 9139 26892 10968 199 271 26696 10697 0 0 9849 3890 31 33 100 98 100 98 30793 37393 2.369 .422 .401 .462 .42 1.644 80 282 .412 .99 100 2100 5750 62 72 73 83 0 12149 350 11799 .545 14161 13811 1.835 .517 -.876 -.951
3 10156 14879 193 266 9963 14613 13003 16994 196 270 12810 16728 0 0 6432 9445 30 32 100 97 98 97 24576 29538 .682 1.467 1.306 1.408 1.487 2.207 80 314 1.48 .98 100 2250 5750 62 72 88 98 0 32531 582 31950 3.207 37156 36574 .312 2.855 1.681 1.514
4 22842 9813 188 265 22654 9548 26649 11437 188 267 26461 11172 0 0 9130 3848 30 33 100 100 100 100 32202 37633 2.373 .421 .422 .426 .419 1.58 80 388 .415 .98 110 2410 5750 61 72 103 114 0 12754 344 12409 .548 14865 14520 1.826 .549 -.868 -.866
5 8238 1592 191 268 8047 1324 9464 1867 191 268 9273 1599 0 0 4528 764 30 35 98 91 98 90 9371 10872 6.078 .165 .172 .173 .167 1.953 80 325 .163 .98 100 2560 5740 61 71 119 129 0 1071 180 891 .111 1256 1076 9.033 .116 -3.175 -3.107
6 16580 27571 191 271 16389 27300 20968 32166 191 271 20777 31895 0 0 9283 16069 29 35 100 98 97 95 43689 52672 .6 1.666 1.535 1.491 1.714 1.898 80 298 1.706 .98 100 2700 5740 61 71 133 143 0 69982 688 69294 4.228 81645 80957 .237 3.896 2.08 1.962
7 1645 1204 186 262 1459 942 2105 1512 189 265 1919 1250 0 0 935 592 28 35 96 91 87 83 2401 3169 1.549 .646 .651 .722 .645 2.279 80 300 .631 .96 100 2850 5750 62 72 148 158 0 1281 279 1002 .687 1608 1330 1.456 .693 -.542 -.529
8 11958 18006 189 265 11769 17741 14269 20311 190 267 14080 20046 0 0 6508 9156 30 34 100 100 100 100 29510 34126 .663 1.507 1.424 1.696 1.479 1.678 80 346 1.488 .99 110 3010 5750 61 72 163 174 0 41022 604 40419 3.434 46274 45670 .291 3.244 1.78 1.698
9 13370 5430 183 264 13187 5166 16177 6326 185 266 15994 6062 0 0 8418 3319 30 35 97 93 95 93 18353 22056 2.553 .392 .379 .394 .391 1.826 80 342 .386 .98 100 3160 5740 61 71 179 189 0 6238 303 5934 .45 7267 6964 2.222 .435 -1.152 -1.2
10 6972 1421 182 261 6790 1160 7653 1542 184 263 7471 1281 0 0 3959 653 28 34 100 98 98 93 7950 8752 5.853 .171 .171 .177 .168 2.024 80 311 .165 .97 100 3310 5750 62 72 194 204 0 945 174 772 .114 1026 852 8.799 .114 -3.137 -3.132
11 16055 27826 187 263 15868 27563 20887 33738 189 265 20700 33475 0 0 11040 18692 33 35 96 97 92 96 43431 54175 .576 1.737 1.617 1.961 1.71 1.866 80 348 1.727 .98 100 3440 5750 62 72 207 217 0 71812 679 71133 4.483 87069 86390 .223 4.173 2.164 2.061
12 2209 1466 189 259 2020 1207 2341 1517 191 262 2152 1258 0 0 523 303 34 33 100 100 100 100 3227 3410 1.674 .598 .585 .602 .606 1.197 52 321 .593 .98 90 3610 5740 61 70 224 233 0 1570 277 1292 .64 1624 1347 1.563 .626 -.644 -.676
13 285 475 185 259 100 216 281 494 188 260 96 235 0 0 53 91 29 34 90 92 76 88 316 331 .463 2.16 2.448 2.233 2.119 2.175 52 269 2.316 .73 80 3760 5740 62 70 240 248 0 397 216 180 1.804 413 196 .554 2.044 .851 1.032
14 231 348 183 257 48 91 233 345 185 257 50 88 0 0 34 48 28 32 71 90 42 75 139 138 .527 1.896 1.76 1.726 1.96 2.732 52 257 2.519 .43 80 3910 5750 63 71 255 263 0 259 191 68 1.409 256 65 .71 1.308 .495 .387
15 377 2229 186 260 191 1969 415 2466 187 261 229 2206 0 0 121 1295 30 34 85 90 80 88 2160 2435 .097 10.309 9.633 7.279 9.754 2.609 80 357 11.156 .93 100 4070 5740 61 71 270 280 0 6786 792 5994 31.384 7507 6716 .032 29.326 4.972 4.874
16 229 377 185 258 44 119 233 375 185 261 48 117 0 0 29 49 28 33 67 94 38 86 163 165 .37 2.705 2.438 2.681 2.359 2.24 52 265 2.747 .49 90 4210 5750 62 71 284 293 0 319 218 101 2.29 317 99 .437 2.063 1.195 1.045
17 241 335 183 253 58 82 235 330 184 255 52 77 0 0 49 57 29 31 76 82 46 63 140 129 .707 1.414 1.481 1.374 1.385 2.616 52 260 1.497 .5 80 4370 5740 62 70 301 309 0 216 163 53 .911 213 50 1.097 .955 -.134 -.067
18 249 405 182 254 67 151 247 404 185 253 65 150 0 0 40 55 29 33 76 98 57 96 218 215 .444 2.254 2.308 2.472 2.048 2.125 52 268 2.631 .56 90 4520 5750 62 71 315 324 0 320 201 119 1.782 319 119 .561 1.825 .834 .868
19 4320 917 179 247 4141 670 5177 1084 179 247 4998 837 0 0 2312 389 28 31 93 93 92 91 4811 5835 6.181 .162 .167 .176 .166 1.9 80 362 .161 .98 100 4670 5740 61 71 330 340 0 555 150 406 .098 657 507 10.204 .101 -3.351 -3.301
20 2491 1027 175 243 2316 784 2758 1141 179 245 2583 898 0 0 766 280 30 32 100 100 100 100 3100 3481 2.954 .339 .348 .339 .35 1.378 52 297 .337 .96 90 4820 5740 61 70 345 354 0 839 198 640 .276 932 733 3.618 .284 -1.855 -1.817

Total number of rows: 44544

Table truncated, full table size 9852 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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