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Sample GSM799010 Query DataSets for GSM799010
Status Public on Jan 12, 2012
Title P39_06_19_07
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 Primary Human Tissue Skin
Organism Homo sapiens
Characteristics tissue: skin
age: 76 years
organism part: posterior neck
disease state: active
individual: 39
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/2007-07/75954.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 GPL9551
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 10543 2909 239 190 10304 2719 10142 2772 248 196 9903 2582 0 0 1390 480 143 43 100 100 100 100 13023 12485 3.79 .264 .261 .262 .266 1.103 80 476 .259 .98 110 1630 5680 82 93 77 88 0 3273 214 3059 .297 3119 2905 3.368 .293 -1.752 -1.769
2 12005 3326 241 190 11764 3136 11730 3276 260 194 11489 3086 0 0 3251 968 182 42 100 100 100 100 14900 14575 3.751 .267 .269 .265 .268 1.281 80 312 .264 .99 110 1780 5680 82 93 92 103 0 3863 221 3642 .31 3804 3584 3.23 .312 -1.692 -1.681
3 9971 9708 238 188 9733 9520 10127 10015 324 243 9889 9827 0 0 1457 1966 697 502 100 100 100 100 19253 19716 1.022 .978 .994 .953 .994 1.219 80 326 .996 .98 110 1930 5680 82 93 107 118 0 21923 425 21498 2.209 22616 22192 .453 2.244 1.143 1.166
4 12714 3486 237 185 12477 3301 12702 3513 328 241 12465 3328 0 0 3041 1008 692 496 100 98 98 96 15778 15793 3.78 .265 .267 .258 .269 1.217 80 336 .278 .89 110 2060 5680 82 93 120 131 0 4079 216 3862 .31 4110 3894 3.231 .312 -1.692 -1.679
5 7232 1094 249 193 6983 901 7092 1090 268 197 6843 897 0 0 1218 182 121 49 100 100 100 100 7884 7740 7.75 .129 .131 .128 .129 1.129 80 253 .128 .98 100 2210 5690 84 94 136 146 0 774 137 637 .091 771 634 10.957 .093 -3.454 -3.431
6 18332 24564 250 193 18082 24371 19410 26990 252 194 19160 26797 0 0 5006 8609 38 36 100 100 100 100 42453 45957 .742 1.348 1.399 1.245 1.374 1.424 120 374 1.403 .98 120 2360 5690 83 95 150 162 0 73408 577 72831 4.028 80658 80081 .248 4.18 2.01 2.063
7 1411 619 239 189 1172 430 1440 644 246 192 1201 455 0 0 225 115 39 33 100 100 100 98 1602 1656 2.726 .367 .379 .358 .374 1.341 80 293 .361 .95 110 2500 5680 82 93 164 175 0 484 148 336 .287 503 356 3.487 .296 -1.802 -1.756
8 10771 10312 246 189 10525 10123 10812 10655 325 240 10566 10466 0 0 1529 2342 750 485 100 100 100 98 20648 21032 1.04 .962 .991 .915 .99 1.394 80 370 .982 .98 110 2640 5680 82 93 178 189 0 23422 429 22992 2.185 24201 23771 .458 2.25 1.127 1.17
9 259 532 252 193 7 339 254 528 335 244 2 335 0 0 51 93 775 501 0 3 0 0 346 337 .021 48.429 167.5 14.846 12.78 2.663 80 346 1.348 .44 110 2810 5690 83 94 195 206 0 1790 649 1141 162.938 1776 1127 .006 563.556 7.348 9.138
10 270 332 249 187 21 145 267 328 251 195 18 141 0 0 44 66 40 101 23 82 6 10 166 159 .145 6.905 7.833 5.921 4.431 3.177 80 255 5.234 .29 100 2970 5690 84 94 212 222 0 458 258 200 9.52 452 194 .105 10.8 3.251 3.433
11 5532 2872 248 195 5284 2677 5430 2848 275 204 5182 2653 0 0 563 355 226 75 100 100 100 100 7961 7835 1.974 .507 .512 .504 .509 1.108 80 296 .501 .98 110 3100 5690 83 94 224 235 0 4034 274 3760 .712 4000 3726 1.405 .719 -.491 -.476
12 404 525 257 198 147 327 404 524 279 212 147 326 0 0 46 62 216 78 7 100 0 100 474 473 .45 2.224 2.218 2.319 2.16 1.502 80 325 .551 .51 110 3250 5690 83 94 239 250 0 588 222 366 2.491 587 365 .402 2.483 1.317 1.312
13 571 697 250 193 321 504 588 712 252 199 338 519 0 0 95 168 38 45 98 100 97 96 825 857 .637 1.57 1.536 1.521 1.603 1.402 80 261 1.639 .93 100 3410 5690 84 94 256 266 0 845 234 611 1.903 863 629 .526 1.861 .928 .896
14 1004 1436 252 195 752 1241 1009 1426 257 198 757 1231 0 0 181 468 37 34 98 100 98 100 1993 1988 .606 1.65 1.626 1.64 1.628 1.321 80 295 1.813 .93 110 3540 5690 83 94 268 279 -100 2423 329 2094 2.784 2406 2077 .359 2.744 1.477 1.456
15 257 217 259 204 -2 13 256 215 260 206 -3 11 0 0 39 35 40 33 13 28 3 5 11 8 null null null .979 .86 3.378 52 148 -1 -1 80 3690 5690 85 93 285 293 0 null null null null null null null null null null
16 3944 2435 260 199 3684 2236 3908 2414 264 201 3648 2215 0 0 387 294 75 45 100 100 100 100 5920 5863 1.648 .607 .607 .604 .615 1.13 80 331 .603 .98 110 3820 5690 83 94 296 307 0 3512 287 3225 .875 3482 3195 1.142 .876 -.192 -.191
17 344 321 261 198 83 123 342 321 257 202 81 123 0 0 57 59 77 75 53 86 13 32 206 204 .675 1.482 1.519 1.583 1.41 2.184 52 221 1.218 .71 80 3980 5690 85 93 314 322 0 231 142 88 1.065 231 88 .939 1.091 .091 .126
18 272 220 260 198 12 22 272 223 258 198 12 25 0 0 33 32 53 49 13 17 0 0 34 37 .545 1.833 2.083 1.228 1.063 3.178 52 210 .918 .63 80 4120 5690 85 93 328 336 0 245 221 25 2.045 249 28 .489 2.324 1.032 1.217
19 247 204 254 198 -7 6 249 202 256 200 -5 4 0 0 30 34 38 36 9 11 0 3 -1 -1 null null null .767 .641 5.47 52 201 1.609 .04 80 4270 5690 85 93 343 351 0 null null null null null null null null null null
20 251 201 257 205 -6 -4 243 204 258 204 -14 -1 0 0 34 22 37 34 9 1 3 0 -10 -15 null null null .599 .61 3.152 52 203 .116 .03 80 4420 5690 85 93 358 366 0 null null null null null null null null null null

Total number of rows: 49152

Table truncated, full table size 10577 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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