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Sample GSM989823 Query DataSets for GSM989823
Status Public on Aug 23, 2012
Title PC 22T
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 22T2
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/2008-09/81255.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 3770 2545 38 48 3732 2496 4307 2804 39 53 4269 2755 0 0 1416 1018 9 18 100 100 100 100 6228 7024 1.495 .669 .645 .655 .671 3.441 80 422 .662 .98 100 1820 7260 17 27 33 43 0 2204 42 2161 .579 2428 2386 1.727 .559 -.788 -.84
2 4086 3508 51 50 4034 3457 4205 3617 55 56 4154 3567 0 0 783 652 17 24 100 100 100 100 7491 7721 1.167 .857 .859 .857 .846 2.723 52 275 .828 .98 90 1960 7260 17 26 47 56 0 3038 43 2993 .742 3132 3089 1.348 .744 -.43 -.427
3 6092 14870 61 59 6030 14811 6342 15271 70 74 6280 15212 0 0 1141 2509 101 123 100 100 100 100 20841 21492 .407 2.456 2.422 2.489 2.439 3.106 52 320 2.404 .97 90 2120 7250 16 25 63 72 0 12876 51 12825 2.127 13223 13172 .47 2.098 1.089 1.069
4 3894 3532 70 59 3824 3473 4047 3762 76 73 3977 3703 0 0 919 950 97 115 100 98 100 98 7297 7680 1.101 .908 .931 .87 .935 3.318 80 343 .894 .98 110 2270 7260 16 27 77 88 0 3058 51 3007 .786 3258 3206 1.272 .806 -.347 -.311
5 303 187 69 57 233 129 298 178 71 60 229 120 0 0 47 50 18 25 100 100 100 96 362 349 1.806 .554 .524 .52 .539 3.661 52 271 .524 .79 90 2410 7250 16 25 92 101 0 162 49 112 .479 154 104 2.086 .454 -1.061 -1.14
6 2576 5525 80 65 2496 5460 2572 5583 87 77 2491 5518 0 0 411 851 38 50 100 100 100 100 7956 8009 .457 2.188 2.215 2.196 2.192 2.71 80 414 2.143 .98 110 2560 7260 16 27 106 117 0 4784 56 4728 1.894 4834 4778 .528 1.918 .922 .94
7 164 135 85 68 78 67 164 129 93 77 78 60 0 0 35 44 30 41 90 65 69 34 145 138 1.164 .859 .769 .768 .888 5.378 52 224 .69 .64 80 2730 7260 18 26 125 133 0 117 59 58 .744 112 52 1.344 .666 -.427 -.586
8 5470 12642 83 57 5387 12584 6198 14563 85 65 6115 14505 0 0 1771 4419 20 39 97 100 96 97 17971 20620 .428 2.336 2.372 2.441 2.346 3.412 80 348 2.354 .98 110 2870 7250 15 26 137 148 0 10947 49 10897 2.023 12610 12560 .494 2.054 1.016 1.038
9 192 121 89 57 103 64 162 111 91 64 72 53 0 0 214 85 19 36 91 61 78 31 167 125 1.609 .621 .736 .73 .683 5.824 80 375 .32 .68 100 3020 7250 16 26 153 163 0 105 49 55 .538 96 46 1.859 .637 -.894 -.65
10 160 99 92 57 68 41 165 91 93 60 72 33 0 0 34 36 20 24 90 56 75 38 109 105 1.659 .603 .458 .544 .61 7.072 80 362 .415 .52 100 3180 7260 17 27 169 179 0 86 49 36 .522 79 29 1.915 .397 -.938 -1.333
11 398 1071 68 57 330 1013 394 1106 71 62 325 1048 0 0 148 379 20 24 97 98 97 98 1343 1373 .326 3.07 3.225 3.06 3.294 3.378 80 309 3.013 .93 100 3330 7250 16 26 184 194 0 927 49 877 2.658 958 907 .376 2.792 1.41 1.481
12 242 995 48 56 194 938 248 1018 51 60 199 961 0 0 61 298 16 22 98 100 97 98 1132 1160 .207 4.835 4.829 4.759 4.773 3.31 80 350 4.858 .94 110 3470 7250 15 26 197 208 0 862 48 812 4.187 882 832 .239 4.182 2.066 2.064
13 184 176 47 54 137 121 188 178 52 62 141 123 0 0 46 64 24 56 97 83 96 53 258 264 1.132 .883 .872 .816 .873 4.219 80 412 1.089 .79 110 3630 7250 15 26 213 224 0 152 47 105 .765 154 107 1.308 .755 -.387 -.405
14 169 205 57 54 112 150 158 192 61 64 101 137 0 0 58 57 27 57 100 97 96 66 262 238 .747 1.339 1.356 1.354 1.364 3.853 80 410 1.461 .85 110 3770 7260 16 27 227 238 0 178 47 130 1.16 166 119 .862 1.175 .214 .232
15 88 73 43 51 45 21 82 64 47 56 39 12 0 0 34 32 17 19 81 35 55 18 66 51 2.143 .467 .308 .478 .428 7.598 80 312 .317 .34 100 3930 7260 17 27 244 254 0 63 44 18 .404 55 10 2.475 .266 -1.307 -1.908
16 942 1452 33 44 908 1408 980 1601 35 48 947 1557 0 0 259 478 7 16 100 100 100 100 2316 2504 .645 1.551 1.644 1.496 1.578 3.338 80 330 1.543 .96 110 4090 7270 17 28 259 270 0 1257 38 1219 1.343 1386 1348 .745 1.424 .425 .51
17 76 56 32 44 43 12 75 53 36 48 42 9 0 0 20 18 15 19 92 27 71 11 55 51 3.583 .279 .214 .358 .407 7.357 80 341 .152 .13 110 4230 7250 15 26 273 284 0 48 38 10 .242 46 8 4.138 .186 -2.049 -2.43
18 42 47 34 45 8 1 40 44 36 48 6 -1 0 0 10 15 15 18 23 14 1 4 9 5 8 .125 null 1.581 1.621 9.288 120 397 .039 .03 120 4380 7250 15 27 288 300 -100 41 39 1 .108 38 -1 9.239 null -3.208 null
19 313 515 34 44 278 470 303 502 36 48 268 458 0 0 61 131 7 18 100 100 100 100 748 726 .591 1.691 1.709 1.666 1.695 2.985 80 296 1.645 .94 110 4530 7260 16 27 303 314 0 446 38 407 1.464 435 397 .683 1.48 .55 .565
20 940 4050 34 44 905 4006 949 4250 35 48 914 4206 0 0 179 876 7 18 100 100 100 100 4911 5120 .226 4.427 4.602 4.354 4.476 2.78 80 310 4.47 .98 110 4690 7260 16 27 319 330 0 3507 38 3469 3.833 3680 3642 .261 3.985 1.938 1.994

Total number of rows: 44544

Table truncated, full table size 9167 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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