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Sample GSM989696 Query DataSets for GSM989696
Status Public on Aug 23, 2012
Title PC 361T2
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 361T2.1
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 72
pre-operation treatment: None
individual: PC 361T
disease free survival: 24.40
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/2008-09/81252.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 11867 7985 37 82 11830 7902 13492 8911 47 103 13454 8829 0 0 4711 2995 94 186 97 98 96 96 19732 22283 1.497 .668 .656 .741 .666 3.052 80 429 .658 .99 100 1790 7370 28 38 30 40 0 7234 74 7159 .605 8073 7998 1.653 .594 -.725 -.75
2 14727 10406 41 81 14686 10325 15339 10512 47 88 15298 10431 0 0 3355 1867 23 42 100 100 100 100 25011 25729 1.422 .703 .682 .718 .697 2.407 52 266 .681 .99 90 1930 7370 28 37 44 53 0 9427 73 9354 .637 9523 9450 1.57 .618 -.651 -.695
3 18626 27949 42 83 18583 27865 22406 32259 51 98 22363 32175 0 0 8630 12180 26 75 100 100 100 100 46448 54538 .667 1.499 1.439 1.616 1.484 2.864 80 359 1.462 .99 100 2100 7360 27 37 61 71 0 25319 75 25243 1.358 29224 29148 .736 1.303 .442 .382
4 12357 8319 40 86 12316 8232 13444 8891 45 96 13403 8805 0 0 4275 2818 17 49 100 98 100 98 20548 22208 1.496 .668 .657 .675 .669 2.288 80 408 .661 .99 110 2250 7360 26 37 75 86 0 7536 78 7457 .606 8054 7977 1.651 .595 -.724 -.749
5 948 359 44 88 904 271 996 378 56 103 952 289 0 0 321 119 71 105 96 90 95 68 1175 1241 3.336 .3 .304 .3 .309 3.63 80 363 .282 .87 100 2400 7360 27 37 91 101 0 325 80 246 .272 342 262 3.682 .275 -1.881 -1.862
6 10363 12797 58 99 10305 12697 10059 12474 78 113 10001 12375 0 0 1633 2101 49 81 100 100 100 100 23002 22376 .812 1.232 1.237 1.231 1.22 2.176 80 298 1.221 .99 110 2540 7370 27 38 104 115 0 11593 90 11502 1.116 11300 11211 .896 1.121 .159 .165
7 190 251 45 92 144 159 224 257 60 102 178 164 0 0 85 116 38 54 79 73 70 62 303 342 .906 1.104 .921 1.181 1.162 4.364 120 388 1.095 .77 120 2700 7370 27 39 120 132 0 227 83 144 1 233 149 1 .835 0 -.261
8 19716 30143 39 89 19676 30053 22098 32634 45 96 22059 32545 0 0 6933 9224 21 54 100 100 100 100 49729 54604 .655 1.527 1.475 1.675 1.506 2.864 80 346 1.489 .99 110 2850 7360 26 37 135 146 0 27307 81 27225 1.384 29564 29483 .723 1.337 .469 .419
9 125 102 39 88 85 14 130 88 42 96 90 0 0 0 32 49 14 52 97 18 92 7 99 90 6.071 .165 null .334 .506 7.114 80 436 .493 .2 110 3000 7380 28 39 150 161 0 92 80 13 .149 80 0 6.702 null -2.745 null
10 88 92 37 85 51 7 89 92 39 92 52 7 0 0 19 39 11 42 96 11 92 1 58 59 7.286 .137 .135 .65 .643 4.742 52 287 .238 .06 90 3170 7360 27 36 168 177 0 83 77 6 .124 83 6 8.042 .122 -3.008 -3.036
11 961 2228 36 78 924 2150 936 2120 37 85 899 2042 0 0 238 535 6 39 100 100 100 100 3074 2941 .43 2.327 2.271 2.339 2.312 2.467 80 276 2.3 .97 110 3300 7370 27 38 180 191 0 2018 71 1948 2.108 1921 1850 .474 2.058 1.076 1.041
12 404 707 35 89 368 618 436 720 105 180 401 630 0 0 197 311 943 1230 0 2 0 0 986 1031 .595 1.679 1.571 1.842 1.651 4.201 120 367 1.636 .95 120 3450 7370 27 39 195 207 0 640 81 560 1.521 652 571 .657 1.423 .605 .509
13 337 274 36 83 301 190 347 260 118 194 311 176 0 0 95 108 1030 1342 0 0 0 0 491 487 1.584 .631 .566 .566 .629 4.265 80 308 .586 .74 110 3600 7360 26 37 210 221 0 248 75 172 .572 236 159 1.749 .513 -.806 -.964
14 154 228 35 76 118 152 155 224 36 86 119 147 0 0 26 62 6 41 100 96 100 88 270 266 .776 1.288 1.235 1.207 1.305 3.53 80 291 1.309 .74 110 3750 7360 26 37 225 236 0 207 69 138 1.167 203 133 .857 1.119 .223 .162
15 47 82 35 82 11 0 46 76 36 90 11 -5 0 0 8 38 7 45 69 7 35 1 11 6 null null null 2.558 2.441 6.343 120 377 -1 -1 120 3900 7360 26 38 240 252 -50 74 74 0 null 69 -5 null null null null
16 2449 4234 36 83 2412 4151 2559 4476 37 90 2522 4392 0 0 776 1317 7 44 100 100 100 98 6563 6914 .581 1.721 1.741 1.715 1.727 2.562 80 306 1.704 .99 110 4060 7360 26 37 256 267 0 3836 75 3760 1.559 4055 3979 .641 1.578 .641 .658
17 85 100 35 83 49 17 88 96 37 89 52 12 0 0 19 42 6 39 93 26 92 7 66 64 2.882 .347 .231 .761 .736 6.458 80 219 .314 .05 100 4210 7370 28 38 272 282 0 91 75 15 .314 87 11 3.182 .209 -1.67 -2.258
18 44 83 36 86 7 -2 43 76 37 90 7 -9 0 0 9 35 7 36 47 12 21 2 5 -2 null null null 3.572 2.849 8.927 120 368 73.223 .04 120 4360 7360 26 38 286 298 -100 75 78 -2 null 69 -8 null null null null
19 747 1668 38 86 708 1581 743 1632 40 95 705 1546 0 0 156 378 9 44 100 100 100 100 2289 2251 .448 2.233 2.193 2.221 2.219 2.402 80 295 2.235 .98 110 4510 7360 26 37 301 312 0 1511 78 1432 2.023 1478 1401 .494 1.987 1.016 .99
20 2663 11350 39 86 2623 11263 2702 11495 40 96 2663 11408 0 0 574 2380 7 46 100 100 100 100 13886 14071 .233 4.294 4.284 4.282 4.263 2.27 80 309 4.284 .99 110 4660 7360 26 37 316 327 0 10282 78 10203 3.89 10413 10335 .257 3.881 1.96 1.956

Total number of rows: 44544

Table truncated, full table size 9292 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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