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Sample GSM989681 Query DataSets for GSM989681
Status Public on Aug 23, 2012
Title PC 575N2
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 575N3
Organism Homo sapiens
Characteristics individual: PC 575N
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/2008-08/81237.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 20269 11121 40 51 20228 11069 19684 11105 44 54 19644 11054 0 0 2433 1620 14 24 100 100 100 100 31297 30698 1.827 .547 .563 .545 .545 2.161 52 180 .55 .99 90 1760 7240 23 32 0 8 0 11618 53 11564 .572 11601 11548 1.749 .588 -.807 -.766
2 14527 7585 41 52 14485 7533 16404 8881 48 58 16362 8828 0 0 5674 3446 32 29 100 100 100 100 22018 25190 1.923 .52 .54 .48 .54 3.31 80 311 .525 .97 100 1910 7250 24 34 14 24 0 7924 54 7870 .543 9278 9222 1.841 .564 -.88 -.827
3 40049 21071 42 51 40007 21019 39974 20801 72 58 39932 20750 0 0 3349 3056 293 44 100 100 100 100 61026 60682 1.903 .525 .52 .521 .52 2.242 52 296 .518 .98 90 2050 7220 21 30 28 37 0 22012 53 21958 .549 21730 21677 1.822 .543 -.865 -.881
4 17028 9006 39 49 16988 8956 17928 9700 63 57 17888 9650 0 0 5103 3163 276 42 97 100 97 100 25944 27538 1.897 .527 .539 .503 .534 2.743 80 333 .532 .99 100 2210 7240 23 33 44 54 0 9408 51 9356 .551 10133 10081 1.816 .564 -.861 -.827
5 1482 246 39 45 1442 201 1482 252 51 51 1442 206 0 0 213 81 79 24 100 100 100 96 1643 1648 7.174 .139 .143 .128 .141 3.322 52 229 .128 .86 90 2350 7230 22 31 58 67 0 257 47 210 .146 263 215 6.867 .149 -2.78 -2.744
6 15359 11619 39 44 15320 11574 16471 13103 48 48 16432 13058 0 0 5367 5187 63 19 100 100 100 100 26894 29490 1.324 .755 .795 .67 .801 3.642 120 360 .778 .97 120 2510 7250 23 35 73 85 0 12138 46 12091 .789 13688 13641 1.267 .83 -.341 -.269
7 377 185 38 45 338 139 367 178 43 49 328 132 0 0 65 68 22 19 100 100 100 94 477 460 2.432 .411 .402 .367 .438 3.71 52 259 .38 .8 90 2660 7230 22 31 89 98 0 193 47 145 .43 186 138 2.328 .42 -1.219 -1.25
8 36669 19404 40 48 36628 19356 37930 20704 47 57 37889 20656 0 0 7765 6518 41 32 100 100 100 100 55984 58545 1.892 .528 .545 .451 .544 3.762 80 323 .542 .98 100 2810 7240 23 33 104 114 0 20271 50 20221 .552 21629 21579 1.811 .57 -.857 -.812
9 325 396 37 45 288 350 337 425 43 54 299 379 0 0 105 172 38 32 97 92 96 91 638 678 .823 1.215 1.268 1.061 1.226 3.894 80 304 1.218 .9 100 2970 7230 22 32 120 130 0 414 47 366 1.27 444 396 .788 1.324 .344 .405
10 267 389 37 44 230 345 269 376 38 49 232 332 0 0 67 125 10 22 100 100 100 100 575 564 .667 1.5 1.431 1.453 1.46 2.917 80 335 1.485 .9 110 3110 7240 22 33 133 144 0 406 46 360 1.567 393 347 .638 1.495 .648 .58
11 1986 1699 38 44 1947 1654 1930 1654 40 49 1892 1610 0 0 584 583 13 21 100 100 100 100 3601 3502 1.177 .85 .851 .8 .889 3.172 80 321 .828 .95 100 3270 7230 22 32 150 160 0 1775 46 1728 .887 1728 1682 1.127 .889 -.172 -.17
12 964 10727 37 42 926 10684 971 11025 39 48 933 10982 0 0 220 3736 9 21 100 100 100 100 11610 11915 .087 11.538 11.771 10.724 11.776 3.1 80 294 12.585 .97 100 3420 7230 22 32 165 175 0 11206 44 11161 12.053 11518 11473 .083 12.297 3.591 3.62
13 920 506 37 41 883 465 954 516 39 48 916 475 0 0 278 251 10 21 100 98 100 95 1348 1391 1.899 .527 .519 .485 .511 3.395 80 307 .512 .88 100 3570 7230 22 32 180 190 0 529 43 486 .55 539 496 1.818 .542 -.862 -.884
14 476 632 37 42 439 589 476 630 39 49 439 587 0 0 113 191 9 24 100 98 98 98 1028 1026 .745 1.342 1.337 1.323 1.325 2.756 80 344 1.304 .92 110 3720 7240 22 33 194 205 0 660 44 615 1.402 658 613 .713 1.397 .487 .482
15 57 82 37 42 19 39 54 78 39 48 16 35 0 0 10 35 7 21 92 69 55 42 58 51 .487 2.053 2.188 2.191 2.491 5.702 52 263 3.236 .4 90 3880 7230 22 31 211 220 0 86 44 41 2.144 81 37 .466 2.285 1.101 1.192
16 6200 3257 37 42 6163 3214 6124 3312 38 48 6087 3270 0 0 1518 1122 7 21 100 100 100 100 9377 9357 1.918 .521 .537 .473 .551 3.387 80 293 .525 .96 100 4020 7230 22 32 225 235 0 3403 44 3358 .545 3460 3416 1.836 .561 -.876 -.833
17 121 285 39 44 82 241 119 275 40 48 80 231 0 0 24 75 9 19 100 100 100 100 323 311 .34 2.939 2.888 2.898 2.912 3.111 52 314 3.07 .82 90 4170 7230 22 31 240 249 0 298 46 252 3.07 287 241 .326 3.017 1.618 1.593
18 56 62 37 41 18 21 54 58 39 48 16 17 0 0 10 27 7 21 88 36 67 15 39 33 .857 1.167 1.063 .935 .93 6.574 52 224 1.457 .18 80 4340 7230 23 31 258 266 0 65 43 22 1.219 61 18 .82 1.11 .285 .151
19 1299 713 36 44 1263 669 1389 787 38 49 1352 743 0 0 601 378 7 22 99 94 98 90 1932 2095 1.888 .53 .55 .457 .557 4.101 120 366 .527 .94 120 4470 7240 22 34 269 281 0 745 46 699 .553 822 776 1.807 .574 -.854 -.801
20 6742 11271 38 42 6704 11228 6675 11826 40 49 6636 11783 0 0 1680 3257 11 24 100 100 100 100 17932 18419 .597 1.675 1.776 1.604 1.734 2.659 80 353 1.665 .97 110 4630 7230 21 32 285 296 0 11775 44 11730 1.75 12354 12309 .572 1.855 .807 .891

Total number of rows: 44544

Table truncated, full table size 9515 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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