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Sample GSM799007 Query DataSets for GSM799007
Status Public on Jan 12, 2012
Title P7_06_15_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 from Skin
Organism Homo sapiens
Characteristics tissue: skin
age: 65 years
organism part: posterior neck
disease state: active
individual: 7
Sex: F
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/2007-07/75948.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 11785 4465 181 438 11604 4027 12439 4741 183 440 12258 4303 0 0 3465 1334 27 69 100 100 100 100 15631 16561 2.882 .347 .351 .341 .35 1.373 80 408 .346 .97 100 1400 5870 114 124 95 105 0 5701 559 5142 .443 6053 5494 2.257 .448 -1.174 -1.158
2 13694 5004 186 444 13508 4560 14081 5263 187 445 13895 4819 0 0 4440 1639 27 64 100 100 100 100 18068 18714 2.962 .338 .347 .336 .345 1.446 80 231 .333 .95 100 1550 5870 114 124 110 120 0 6390 567 5823 .431 6721 6154 2.32 .443 -1.214 -1.175
3 12923 9698 187 455 12736 9243 14882 11434 211 476 14695 10979 0 0 4583 3835 287 318 98 97 98 95 21979 25674 1.378 .726 .747 .697 .753 1.871 80 315 .745 .96 110 1680 5870 113 124 122 133 0 17879 839 17040 1.338 21080 20241 .747 1.377 .42 .462
4 15555 5639 199 460 15356 5179 16214 5820 227 488 16015 5360 0 0 4634 1663 298 319 100 98 100 96 20535 21375 2.965 .337 .335 .335 .342 1.337 80 314 .338 .98 100 1840 5870 114 124 139 149 0 7280 594 6687 .435 7514 6920 2.297 .432 -1.199 -1.211
5 8943 1100 204 460 8739 640 8802 1064 319 484 8598 604 0 0 1205 197 885 124 100 98 100 94 9379 9202 13.655 .073 .07 .069 .072 1.468 52 261 .073 .93 90 1980 5860 113 122 153 162 0 639 267 372 .043 618 351 23.498 .041 -4.554 -4.615
6 30559 30821 199 472 30360 30349 30697 30868 292 517 30498 30396 0 0 3326 5266 758 324 100 100 100 100 60709 60894 1 1 .997 .987 1.032 1.214 80 357 1.045 .96 110 2130 5870 113 124 167 178 0 70708 1083 69625 2.293 70816 69733 .436 2.286 1.197 1.193
7 1412 975 190 458 1222 517 1513 1016 206 503 1323 558 0 0 352 202 92 345 98 83 97 12 1739 1881 2.364 .423 .422 .409 .429 1.5 80 287 .439 .86 100 2280 5870 114 124 183 193 0 1032 485 547 .448 1076 591 2.233 .446 -1.159 -1.163
8 14237 11105 184 434 14053 10671 15766 12021 185 442 15582 11587 0 0 4410 3288 31 71 100 100 100 100 24724 27169 1.317 .759 .744 .766 .762 1.453 80 288 .755 .98 100 2430 5870 114 124 198 208 0 21100 825 20276 1.443 22841 22016 .693 1.413 .529 .499
9 194 551 176 421 18 130 189 551 179 426 13 130 0 0 37 77 28 69 32 78 8 45 148 143 .138 7.222 10 5.463 4.73 3.645 80 245 15.391 .17 100 2580 5880 115 125 213 223 0 529 405 125 6.94 529 125 .144 9.609 2.795 3.264
10 202 663 181 449 21 214 203 672 189 501 22 223 0 0 28 83 87 438 1 1 0 0 235 245 .098 10.19 10.136 8.785 7.815 3.019 80 240 16.986 .26 100 2720 5880 115 125 227 237 0 837 567 270 12.862 848 281 .078 12.794 3.685 3.677
11 6452 6572 186 466 6266 6106 6611 6463 188 464 6425 5997 0 0 1049 809 24 73 100 100 100 100 12372 12422 1.026 .974 .933 .986 .952 1.224 80 262 .965 .97 100 2860 5880 115 125 241 251 0 13133 931 12202 1.947 12916 11984 .514 1.865 .962 .899
12 342 673 181 457 161 216 339 672 184 460 158 215 0 0 36 79 27 68 100 97 100 82 377 373 .745 1.342 1.361 1.28 1.398 1.574 80 362 1.748 .78 110 3010 5870 113 124 255 266 0 635 431 204 1.266 634 203 .79 1.284 .341 .361
13 689 955 180 457 509 498 673 963 180 460 493 506 0 0 77 108 27 97 100 100 100 100 1007 999 1.022 .978 1.026 .965 .967 1.263 52 238 1.101 .87 90 3170 5870 114 123 272 281 0 1287 616 671 1.319 1298 682 .758 1.383 .399 .468
14 1193 2756 180 455 1013 2301 1189 2818 181 464 1009 2363 0 0 177 554 22 104 100 100 100 100 3314 3372 .44 2.271 2.342 2.214 2.283 1.256 52 187 2.435 .96 90 3310 5870 114 123 286 295 0 6966 1150 5816 5.741 7123 5973 .174 5.919 2.521 2.565
15 197 470 179 451 18 19 196 470 182 451 17 19 0 0 26 70 28 66 34 19 7 9 37 36 .947 1.056 1.118 2.572 3.207 3.413 52 197 70.064 .03 80 3440 5870 115 123 300 308 0 181 173 7 .406 181 7 2.465 .43 -1.302 -1.219
16 4357 2152 178 452 4179 1700 4620 2221 181 459 4442 1769 0 0 1197 393 26 71 100 100 100 100 5879 6211 2.458 .407 .398 .425 .399 1.377 80 274 .386 .96 100 3600 5880 115 125 315 325 0 2703 568 2135 .511 2790 2222 1.957 .5 -.969 -.999
17 247 574 184 457 63 117 252 585 187 464 68 128 0 0 33 85 26 66 88 71 63 46 180 196 .538 1.857 1.882 1.654 1.84 2.562 80 359 4.558 .43 110 3740 5860 112 123 328 339 0 388 309 79 1.255 395 86 .797 1.272 .327 .347
18 201 471 183 455 18 16 200 461 187 458 17 6 0 0 27 66 24 66 38 23 7 3 34 23 1.125 .889 .353 2.312 2.422 3.051 52 205 55.829 .04 80 3880 5870 115 123 344 352 0 173 167 6 .327 169 2 3.062 .13 -1.614 -2.947
19 183 441 174 429 9 12 179 443 177 430 5 14 0 0 23 66 25 73 23 11 3 3 21 19 .75 1.333 2.8 4.609 7.548 3.11 52 194 14.75 .19 80 4030 5870 115 123 359 367 0 240 233 7 .725 241 8 1.379 1.523 -.464 .607
20 178 440 174 418 4 22 180 433 175 420 6 15 0 0 26 65 26 62 17 19 3 5 26 21 .182 5.5 2.5 2.272 2.322 4.574 52 199 17.288 .11 80 4170 5870 115 123 373 381 0 470 447 24 5.876 463 16 .17 2.671 2.555 1.417

Total number of rows: 49152

Table truncated, full table size 10584 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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