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Sample GSM989716 Query DataSets for GSM989716
Status Public on Aug 23, 2012
Title PC 455N
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 455N2
Organism Homo sapiens
Characteristics individual: PC 455N
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/2008-08/81194.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 GPL9497
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
1 944 2315 36 45 908 2270 1085 2648 36 50 1049 2602 0 0 422 920 3 22 100 100 100 100 3178 3651 .4 2.5 2.48 2.95 2.423 2.592 52 279 2.487 .96 80 1540 6320 20 28 18 26 0 1897 37 1861 2.049 2170 2133 .488 2.033 1.035 1.024
2 1867 4487 36 46 1831 4440 2220 5272 36 49 2184 5226 0 0 793 1652 3 19 100 100 98 100 6271 7410 .412 2.425 2.393 3.122 2.386 3.124 52 241 2.4 .97 80 1690 6320 20 28 33 41 0 3678 38 3639 1.987 4321 4283 .503 1.961 .991 .972
3 8784 15672 36 49 8747 15622 10829 19058 36 52 10792 19008 0 0 3562 6696 4 21 100 100 100 100 24369 29800 .56 1.786 1.761 1.595 1.783 2.179 52 271 1.815 .98 80 1840 6310 19 27 48 56 0 12845 40 12804 1.464 15620 15579 .683 1.444 .55 .53
4 3804 8729 36 47 3767 8681 4560 10541 36 50 4523 10493 0 0 1561 3541 4 19 100 100 100 100 12448 15016 .434 2.304 2.32 2.185 2.236 2.041 52 271 2.317 .98 80 1990 6310 19 27 63 71 0 7154 39 7115 1.889 8640 8600 .529 1.901 .917 .927
5 291 190 36 50 254 139 288 187 37 54 251 136 0 0 36 58 4 19 100 96 100 90 393 387 1.827 .547 .542 .475 .549 2.412 32 212 .573 .87 70 2140 6310 19 26 78 85 0 156 41 114 .449 153 111 2.23 .444 -1.157 -1.171
6 3731 8561 41 64 3689 8497 5066 11799 46 73 5024 11735 0 0 2392 5458 14 43 100 97 100 95 12186 16759 .434 2.303 2.336 2.222 2.301 2.401 80 389 2.313 .99 110 2290 6310 17 28 91 102 0 7017 52 6964 1.888 9671 9618 .53 1.914 .917 .937
7 91 107 37 53 53 54 95 96 44 68 57 43 0 0 26 48 59 85 48 26 0 1 107 100 .981 1.019 .754 .894 1.006 3.767 52 255 1.498 .37 80 2440 6310 19 27 108 116 0 88 43 44 .835 79 35 1.197 .618 -.26 -.694
8 10677 18243 36 52 10640 18190 11937 20407 37 57 11900 20355 0 0 3396 5287 7 36 100 100 100 100 28830 32255 .585 1.71 1.711 1.807 1.696 2.038 52 288 1.7 .98 80 2600 6310 19 27 124 132 0 14952 43 14909 1.401 16726 16683 .714 1.402 .487 .487
9 58 104 35 44 23 59 59 99 36 50 24 55 0 0 10 43 7 35 93 68 78 25 82 79 .39 2.565 2.292 2.426 2.826 2.618 32 223 4.924 .63 70 2760 6300 18 25 140 147 0 85 36 48 2.102 81 45 .476 1.878 1.072 .909
10 60 107 35 37 25 69 60 107 35 45 25 69 0 0 7 32 3 25 100 93 100 68 94 94 .362 2.76 2.76 2.693 2.94 2.009 32 210 4.282 .69 70 2900 6300 18 25 154 161 0 88 30 57 2.262 88 57 .442 2.262 1.178 1.178
11 76 123 35 37 41 85 74 120 35 41 39 83 0 0 14 34 2 15 100 96 100 96 126 122 .482 2.073 2.128 1.995 2.133 2.142 32 219 2.931 .74 70 3060 6300 18 25 170 177 0 101 30 70 1.699 98 68 .589 1.744 .765 .803
12 108 893 35 42 73 851 110 926 35 46 74 884 0 0 21 262 3 22 100 100 100 100 924 958 .086 11.658 11.946 11.583 11.662 1.634 32 227 12.82 .94 70 3200 6300 18 25 184 191 0 732 34 697 9.555 759 725 .105 9.791 3.256 3.291
13 92 123 35 42 57 80 93 125 35 48 58 83 0 0 19 39 5 27 100 90 100 73 137 141 .713 1.404 1.431 1.312 1.463 2.141 52 285 1.646 .83 80 3360 6300 18 26 200 208 0 101 34 66 1.15 102 68 .869 1.173 .202 .23
14 77 117 34 39 43 77 80 121 35 46 46 82 0 0 18 42 5 38 96 75 92 53 120 128 .558 1.791 1.783 1.641 1.773 2.484 52 266 2.19 .77 80 3510 6300 18 26 215 223 0 96 32 63 1.468 99 67 .681 1.461 .554 .547
15 41 44 35 38 6 5 40 42 35 43 5 3 0 0 8 21 3 17 55 18 35 5 11 8 1.2 .833 .6 2.187 1.966 4.15 80 376 10.157 .27 100 3660 6300 17 27 229 239 -50 36 31 4 .683 34 2 1.464 .492 -.55 -1.024
16 335 559 35 39 300 519 369 600 36 43 334 560 0 0 101 146 3 15 100 100 100 100 819 894 .578 1.73 1.677 1.806 1.705 1.627 52 223 1.712 .97 80 3820 6300 18 26 246 254 0 458 32 425 1.418 492 459 .705 1.374 .504 .459
17 46 69 35 43 11 26 46 66 35 46 11 23 0 0 9 41 3 22 71 51 63 20 37 34 .423 2.364 2.091 2.728 2.75 3.576 80 289 7.453 .45 100 3970 6290 16 26 260 270 0 57 35 21 1.937 54 19 .516 1.714 .954 .777
18 39 47 34 42 5 5 39 46 35 45 5 4 0 0 4 18 2 16 60 22 47 6 10 9 1 1 .8 2.453 2.457 3.677 80 289 31.515 .12 100 4120 6290 16 26 275 285 -50 39 34 4 .82 38 3 1.22 .656 -.287 -.609
19 100 119 35 41 64 78 96 110 35 44 61 69 0 0 22 45 2 15 100 94 100 84 142 130 .821 1.219 1.131 1.013 1.052 2.542 52 232 1.441 .8 80 4270 6290 17 25 291 299 0 98 34 64 .999 90 57 1.001 .927 -.002 -.109
20 280 1112 34 41 246 1071 314 1261 35 44 280 1220 0 0 119 536 2 18 100 98 100 98 1317 1500 .23 4.354 4.357 4.117 4.252 2.116 52 243 4.477 .97 80 4420 6290 17 25 306 314 0 911 34 878 3.568 1034 1000 .28 3.571 1.835 1.836

Total number of rows: 44544

Table truncated, full table size 9156 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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