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Sample GSM989732 Query DataSets for GSM989732
Status Public on Aug 23, 2012
Title PC 450N2
Sample type RNA
 
Channel 1
Source name reference RNA
Organism Homo sapiens
Characteristics reference: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PC 450N2.1
Organism Homo sapiens
Characteristics individual: PC 450N
disease state: Normal
tissue: prostate
Growth protocol All prostate samples used for this study were collected at the Stanford University Medical Center between 1999 and 2007 with patient's informed consent under an Institutional Review Board (IRB)-approved protocol. Multiple tissue samples were harvested from each prostate, flash-frozen and stored at 80oC. Frozen sections of each prostate sample were performed and evaluated by a genitourinary pathologist (JKM). The tumor and nontumor areas were marked and contaminating tissues were trimmed away from the block as described previously.48 Tumor samples in which at least 90% of the epithelial cells were cancerous were selected for extraction of DNA and RNA. In total, we selected 98 tumors from 86 patients that met these criteria. Associated clinical data were collected and included preoperative PSA levels, clinical stage, pathological stage, tumor Gleason grade and clinical follow-up. Recurrence was defined as a measurable serum PSA (>0.1ng/ml on two consecutive measurements) after surgery.
Gene-expression profiling was performed as reported. Briefly, Cy5-labeled cDNA was prepared by using 50ug of total RNA from prostate samples and Cy3-labeled cDNA was prepared by using common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines. For each experimental sample, Cy5- and Cy3-labeled samples were cohybridized to HEEBO spotted microarrays.49 HEEBO microarrays were manufactured in the Stanford Functional Genomics Facility at Stanford University and contained 44-544 70-mer probes.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol After hybridization, microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments-Molecular Devices, LLC, Sunnyvale, CA, USA). Fluorescence ratios for array elements were extracted using GENEPIX software and uploaded into the Stanford Microarray Database for subsequent analysis.
Description Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81302.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 Aug 21, 2012
Last update date Aug 23, 2012
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 GPL15971
Series (1)
GSE40272 Gene-expression profiling of prostate tumors

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 21587 36525 72 69 21514 36456 24369 39783 79 80 24296 39714 0 0 8591 15116 30 50 100 100 98 100 57970 64010 .59 1.695 1.635 1.76 1.674 3.031 80 429 1.711 .97 100 1770 6750 30 40 24 34 0 34329 65 34264 1.593 37391 37327 .628 1.536 .671 .619
2 23233 37514 74 67 23159 37446 24711 39046 83 87 24637 38978 0 0 5757 9987 34 87 100 100 100 100 60605 63615 .618 1.617 1.582 1.618 1.614 1.935 52 286 1.64 .98 90 1920 6740 29 38 39 48 0 35259 63 35195 1.52 36699 36635 .658 1.487 .604 .572
3 30976 48764 74 82 30902 48681 35794 56399 85 97 35720 56317 0 1 13894 22814 36 87 100 100 100 100 79583 92037 .635 1.575 1.577 1.567 1.6 3.02 80 296 1.593 .97 100 2090 6750 30 40 56 66 0 45833 77 45755 1.481 53009 52931 .675 1.482 .566 .567
4 19837 29142 64 65 19772 29077 19673 28834 75 82 19609 28769 0 0 3860 7709 43 64 100 100 100 100 48849 48378 .68 1.471 1.467 1.436 1.482 1.826 80 322 1.511 .98 110 2220 6740 28 39 68 79 0 27390 61 27329 1.382 27101 27040 .723 1.379 .467 .464
5 1183 521 69 67 1113 453 1171 489 85 102 1101 421 0 0 293 197 65 138 100 93 100 80 1566 1522 2.457 .407 .382 .377 .379 2.328 80 306 .409 .88 110 2370 6740 28 39 83 94 0 490 63 426 .383 460 396 2.614 .359 -1.386 -1.476
6 13206 17751 85 94 13120 17656 12467 16770 119 138 12381 16675 0 0 3181 5079 131 168 100 100 100 100 30776 29056 .743 1.346 1.347 1.329 1.344 1.722 80 305 1.369 .97 110 2520 6740 28 39 98 109 0 16684 88 16595 1.265 15762 15673 .791 1.266 .339 .34
7 411 409 74 67 336 341 404 391 98 98 329 323 0 0 86 157 120 104 100 93 86 80 677 652 .985 1.015 .982 .927 1.008 2.744 80 283 .865 .74 110 2680 6750 29 40 114 125 0 384 63 321 .954 367 304 1.048 .923 -.068 -.116
8 27986 39086 62 59 27923 39026 30247 42586 65 72 30185 42527 0 0 13864 19445 21 50 100 100 100 100 66949 72712 .715 1.398 1.409 1.391 1.393 2.594 120 362 1.395 .98 120 2830 6740 28 40 129 141 0 36736 55 36680 1.314 40026 39970 .761 1.324 .394 .405
9 325 342 59 57 265 284 317 310 64 69 257 252 0 0 89 157 21 41 100 98 100 88 549 509 .933 1.072 .981 .943 .977 3.132 80 299 1.149 .74 110 2980 6740 28 39 144 155 0 321 54 267 1.007 291 237 .993 .922 .01 -.118
10 423 484 57 56 366 428 406 469 61 67 349 413 0 0 102 171 17 41 100 100 100 100 794 762 .855 1.169 1.183 1.106 1.127 2.335 80 314 1.152 .86 110 3130 6740 28 39 159 170 0 455 53 402 1.099 441 388 .91 1.112 .136 .153
11 1499 2148 59 62 1440 2085 1421 2038 61 71 1361 1976 0 0 443 784 17 46 100 100 100 100 3525 3337 .691 1.448 1.452 1.407 1.445 1.946 80 325 1.475 .96 110 3280 6730 27 38 174 185 0 2019 58 1960 1.361 1915 1857 .735 1.365 .445 .448
12 1089 8524 59 61 1030 8463 1034 7750 62 77 975 7688 0 0 346 2919 19 57 100 100 100 100 9493 8663 .122 8.217 7.885 8.173 8.052 2.014 80 324 9.003 .93 110 3420 6730 27 38 188 199 0 8012 57 7954 7.723 7284 7226 .129 7.411 2.949 2.89
13 822 726 58 60 764 666 813 710 62 75 754 650 0 0 221 217 21 59 100 100 100 100 1430 1404 1.147 .872 .862 .862 .901 2.201 80 310 .809 .9 100 3570 6730 28 38 204 214 0 682 56 626 .819 667 611 1.221 .81 -.287 -.304
14 587 923 58 57 529 865 573 923 62 72 515 865 0 0 127 293 21 50 100 100 100 100 1394 1380 .612 1.635 1.68 1.569 1.613 2.151 80 295 1.648 .92 110 3730 6730 27 38 219 230 0 868 54 813 1.537 868 813 .651 1.579 .62 .659
15 95 64 59 70 35 -6 87 50 64 83 27 -19 0 0 30 39 26 53 50 8 24 1 29 8 null null null .817 .795 6.616 120 348 2.403 .07 120 3880 6730 27 39 234 246 -100 60 66 -6 null 47 -18 null null null null
16 3755 5411 62 74 3692 5337 3528 5455 66 85 3466 5381 0 0 1129 1818 27 55 100 100 100 100 9029 8847 .692 1.446 1.553 1.39 1.432 1.951 80 278 1.446 .98 110 4040 6730 27 38 250 261 0 5086 70 5016 1.359 5127 5058 .736 1.459 .442 .545
17 247 231 60 64 186 167 244 222 65 75 184 157 0 0 102 141 21 50 89 78 85 62 353 341 1.114 .898 .853 .894 .972 3.468 120 335 .994 .7 120 4180 6720 26 38 264 276 0 217 60 157 .844 209 148 1.185 .802 -.245 -.318
18 82 70 63 67 19 2 79 55 66 81 16 -12 0 0 23 46 20 53 40 15 17 5 21 4 9.5 .105 null 1.817 1.902 5.851 120 302 -1 -1 120 4330 6720 26 38 279 291 -100 66 63 2 .099 52 -11 10.108 null -3.337 null
19 1283 1480 65 76 1217 1403 1152 1428 68 88 1087 1351 0 0 419 521 20 56 100 100 100 100 2620 2438 .867 1.153 1.243 1.135 1.177 1.963 80 312 1.133 .96 110 4480 6720 26 37 294 305 0 1391 71 1319 1.084 1342 1270 .923 1.168 .116 .224
20 5504 24197 65 71 5438 24126 5445 23122 70 93 5379 23050 0 0 1115 5184 28 86 100 100 100 100 29564 28429 .225 4.437 4.285 4.417 4.456 1.729 80 327 4.416 .98 110 4630 6720 26 37 309 320 0 22742 67 22676 4.17 21732 21664 .24 4.028 2.06 2.01

Total number of rows: 44544

Table truncated, full table size 9782 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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