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Sample GSM989812 Query DataSets for GSM989812
Status Public on Aug 23, 2012
Title PC 21T2
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 21T2.0
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 62
pre-operation treatment: None
individual: PC 26T
disease free survival: 60.30
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/2008-08/81245.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 6666 3258 48 60 6617 3198 9499 4056 51 78 9451 3996 0 0 4876 2505 13 65 92 80 89 77 9815 13447 2.069 .483 .423 .532 .465 4.669 120 584 .475 .95 120 1790 7320 26 38 41 53 0 3625 67 3558 .538 4513 4446 1.86 .47 -.895 -1.088
2 6226 3841 52 54 6173 3786 5607 3548 60 82 5555 3493 0 0 5677 3568 37 87 75 73 72 65 9959 9048 1.63 .613 .629 .856 .631 5.442 120 411 .605 .97 120 1940 7320 26 38 56 68 0 4273 60 4212 .682 3947 3886 1.466 .7 -.551 -.515
3 13714 5568 56 64 13658 5503 15664 6359 61 90 15608 6295 0 0 5149 2417 26 96 100 95 100 92 19161 21903 2.482 .403 .403 .353 .397 3.699 80 310 .402 .97 100 2110 7310 26 36 74 84 0 6195 71 6122 .448 7075 7004 2.231 .449 -1.158 -1.156
4 7686 5420 53 71 7633 5348 10126 6867 56 86 10073 6795 0 0 4888 3722 18 63 94 85 90 82 12981 16868 1.427 .701 .675 .722 .702 4.151 120 438 .709 .97 120 2250 7310 25 37 87 99 0 6030 79 5950 .78 7640 7560 1.283 .751 -.359 -.414
5 589 112 59 78 530 34 621 91 69 96 561 13 0 0 172 79 37 72 97 23 95 10 564 574 15.588 .064 .023 .092 .103 6.943 80 403 .043 .15 110 2400 7320 26 37 102 113 0 125 87 38 .071 101 14 14.011 .026 -3.808 -5.278
6 8764 6456 76 78 8688 6378 8619 6443 99 98 8543 6365 0 0 1204 1190 72 76 100 100 100 100 15066 14908 1.362 .734 .745 .723 .725 2.39 80 424 .712 .97 110 2550 7320 26 37 117 128 0 7183 87 7096 .817 7168 7081 1.224 .829 -.292 -.271
7 205 139 98 85 107 54 201 127 114 102 102 42 0 0 54 85 56 71 81 31 43 15 161 144 1.981 .505 .412 .519 .55 7.512 32 145 .314 .13 60 2710 7340 31 37 136 142 0 155 95 60 .561 141 47 1.781 .458 -.833 -1.126
8 16306 6757 62 64 16243 6692 17661 7193 74 91 17599 7129 0 0 4390 2306 48 71 100 100 100 100 22935 24728 2.427 .412 .405 .413 .408 2.822 80 333 .407 .96 100 2850 7310 26 36 148 158 0 7518 71 7445 .458 8003 7931 2.182 .451 -1.125 -1.15
9 156 144 54 78 101 65 164 120 59 98 109 42 0 0 68 91 38 78 72 36 63 19 166 151 1.554 .644 .385 .871 .834 7.147 120 339 .62 .31 120 3000 7330 27 39 162 174 0 160 87 72 .716 134 47 1.397 .429 -.482 -1.222
10 207 190 56 76 150 113 212 164 57 96 156 87 0 0 54 119 14 79 98 51 98 31 263 243 1.327 .753 .558 .631 .823 7.615 80 312 .955 .38 110 3150 7320 26 37 177 188 0 211 85 126 .838 182 97 1.193 .62 -.255 -.689
11 1005 798 57 67 947 731 987 766 59 90 929 699 0 0 255 329 14 74 100 98 100 97 1678 1628 1.295 .772 .752 .732 .788 3.33 80 350 .738 .88 100 3300 7310 26 36 193 203 0 888 75 813 .859 852 778 1.164 .837 -.22 -.256
12 732 724 55 68 676 655 742 755 58 93 686 687 0 0 166 267 16 82 100 98 100 96 1331 1373 1.032 .969 1.001 .926 .918 3.051 80 363 .997 .87 110 3460 7310 25 36 208 219 0 805 76 729 1.078 840 764 .928 1.114 .108 .156
13 420 198 55 72 365 126 428 189 86 197 373 116 0 0 98 109 349 1136 66 0 0 0 491 489 2.897 .345 .311 .323 .372 4.796 80 305 .349 .33 110 3600 7320 26 37 222 233 0 220 80 140 .384 210 129 2.604 .346 -1.381 -1.531
14 173 190 55 65 118 124 182 174 78 170 126 108 0 0 59 119 304 990 0 0 0 0 242 234 .952 1.051 .857 1.072 1.102 4.778 120 403 3.309 .95 120 3760 7320 26 38 238 250 0 211 72 138 1.169 194 120 .855 .954 .225 -.069
15 52 69 54 64 -2 5 51 50 56 87 -3 -13 0 0 11 49 15 67 5 15 2 1 3 -16 null null null 4.324 3.386 5.811 120 426 25.871 .15 120 3910 7310 25 37 253 265 -50 77 71 6 null 56 -14 null null null null
16 1220 330 56 67 1164 263 1294 337 56 85 1238 270 0 0 446 170 15 61 98 90 98 78 1427 1508 4.426 .226 .218 .211 .207 3.851 80 248 .204 .75 100 4060 7300 25 35 269 279 0 367 75 293 .251 375 300 3.978 .243 -1.992 -2.043
17 144 148 53 78 90 69 150 120 55 100 96 42 0 0 61 106 14 79 83 40 73 19 159 138 1.304 .767 .438 .949 .963 6.762 120 300 1.476 .39 120 4210 7310 25 37 283 295 0 165 87 77 .853 134 47 1.172 .487 -.229 -1.039
18 51 71 55 75 -3 -4 51 54 58 108 -4 -20 0 0 12 52 23 200 2 0 0 0 -7 -24 null null null 4.302 3.457 5.936 120 326 33.76 .11 120 4360 7310 25 37 298 310 -50 79 83 -4 null 60 -22 null null null null
19 680 373 58 63 621 309 670 357 59 85 611 294 0 0 111 153 17 67 100 95 100 85 930 905 2.01 .498 .481 .432 .484 3.547 80 279 .428 .75 110 4510 7310 25 36 313 324 0 415 70 344 .554 397 327 1.806 .535 -.853 -.901
20 2818 3371 58 64 2760 3306 2769 3336 61 86 2711 3272 0 0 436 732 16 65 100 100 100 100 6066 5983 .835 1.198 1.207 1.183 1.224 2.329 80 286 1.189 .96 110 4660 7310 25 36 328 339 0 3750 71 3678 1.333 3712 3640 .75 1.343 .414 .425

Total number of rows: 44544

Table truncated, full table size 9491 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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