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Sample GSM989733 Query DataSets for GSM989733
Status Public on Aug 23, 2012
Title PC 335T
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 PT 335
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 61
pre-operation treatment: None
individual: PC 21T
disease free survival: 88.37
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/2008-11/81790.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 GPL15972
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 6109 4926 73 80 6035 4845 6495 6279 79 87 6422 6198 0 0 5244 4114 29 36 100 97 97 96 10880 12620 1.246 .803 .965 .879 .783 3.156 80 577 .766 .91 110 1510 7050 31 42 29 40 0 4589 75 4513 .748 5849 5774 1.337 .899 -.419 -.154
2 10236 8471 54 68 10182 8402 12373 10227 58 73 12319 10159 0 0 4037 3603 14 29 100 100 100 98 18584 22478 1.212 .825 .825 .689 .803 3.707 52 270 .813 .9 80 1680 7050 33 41 48 56 0 7891 63 7827 .769 9527 9463 1.301 .768 -.38 -.38
3 12618 36793 56 74 12561 36719 14128 43976 60 86 14072 43901 0 0 3562 14577 21 54 100 100 100 100 49280 57973 .342 2.923 3.12 2.362 3.022 2.895 52 304 3.246 .93 90 1830 7050 32 41 62 71 0 34274 69 34205 2.723 40965 40895 .367 2.906 1.445 1.539
4 12136 9525 61 64 12075 9460 14211 11386 154 210 14150 11321 0 0 4570 3825 1159 1822 98 90 92 86 21535 25471 1.276 .783 .8 .708 .772 3.181 52 257 .821 .91 80 1980 7050 33 41 78 86 0 8873 60 8812 .73 10606 10546 1.37 .745 -.454 -.424
5 590 388 55 58 534 329 664 391 58 63 609 332 0 0 209 102 15 28 96 100 96 100 863 941 1.623 .616 .545 .765 .58 3.619 52 205 .546 .88 80 2140 7050 33 41 94 102 0 361 54 306 .574 364 309 1.742 .508 -.801 -.978
6 3027 5437 55 61 2972 5375 607 1125 62 76 551 1063 0 0 3474 6088 29 55 100 100 100 100 8347 1614 .553 1.809 1.929 1.855 1.772 2.026 156 610 1.821 .94 140 2290 7050 30 44 106 120 0 5065 57 5007 1.685 1048 990 .594 1.797 .753 .846
7 203 271 64 85 139 186 199 229 74 103 134 144 0 0 54 130 37 71 92 96 92 50 325 278 .747 1.338 1.075 1.325 1.088 2.427 52 187 2.276 .7 80 2440 7060 34 42 124 132 0 252 79 173 1.247 213 134 .802 1.001 .318 .002
8 13386 37896 61 81 13325 37814 15153 43611 66 93 15092 43529 0 0 4161 14678 24 54 100 100 100 100 51139 58621 .352 2.838 2.884 2.392 2.816 2.271 52 284 3.124 .93 90 2590 7050 32 41 138 147 0 35301 75 35225 2.644 40625 40549 .378 2.687 1.402 1.426
9 122 152 50 53 71 98 121 154 53 60 70 101 0 0 34 59 14 29 96 88 90 73 169 171 .724 1.38 1.443 1.307 1.206 2.452 52 248 1.596 .75 80 2750 7040 32 40 155 163 0 142 49 91 1.286 143 94 .778 1.344 .363 .427
10 201 269 49 49 151 219 203 263 50 53 154 213 0 0 30 52 9 17 100 100 100 100 370 367 .689 1.45 1.383 1.431 1.449 1.471 32 206 1.595 .86 70 2890 7040 32 39 169 176 0 251 46 204 1.351 245 198 .74 1.288 .434 .366
11 857 1702 52 53 804 1648 933 1836 53 58 880 1782 0 0 261 497 9 35 100 100 100 100 2452 2662 .488 2.05 2.025 2.064 1.984 2.151 52 297 2.173 .9 90 3050 7040 31 40 184 193 0 1585 49 1535 1.909 1710 1660 .524 1.886 .933 .916
12 644 1493 50 51 594 1442 736 1644 52 56 686 1593 0 0 235 511 9 38 100 100 98 98 2036 2279 .412 2.428 2.322 2.477 2.274 2.417 52 257 2.777 .85 80 3190 7040 32 40 199 207 0 1391 48 1343 2.261 1531 1484 .442 2.163 1.177 1.113
13 284 228 47 45 237 182 312 254 47 48 265 208 0 0 110 81 8 21 98 94 96 86 419 473 1.302 .768 .785 .818 .712 2.905 52 275 .744 .87 80 3350 7040 32 40 215 223 0 212 42 170 .715 237 194 1.398 .731 -.483 -.452
14 167 276 47 42 120 234 180 294 48 45 133 252 0 0 48 88 8 15 98 98 98 96 354 385 .513 1.95 1.895 1.801 1.847 2.188 52 271 2.053 .88 80 3500 7040 32 40 230 238 0 257 39 218 1.816 274 235 .551 1.765 .861 .82
15 59 65 47 43 11 22 60 67 47 43 12 23 0 0 8 19 7 12 65 65 31 40 33 35 .5 2 1.917 1.851 2.037 3.518 32 171 3.672 .41 60 3640 7030 32 38 245 251 0 61 40 20 1.863 62 21 .537 1.785 .898 .836
16 1402 3346 47 42 1355 3304 1594 3540 47 45 1547 3497 0 0 501 636 7 21 98 100 96 100 4659 5044 .41 2.438 2.261 3.157 2.25 3.638 52 246 2.397 .92 80 3800 7040 32 40 260 268 0 3117 39 3078 2.271 3298 3258 .44 2.106 1.184 1.074
17 190 286 46 41 144 244 206 285 47 44 160 243 0 0 52 63 9 14 98 100 92 100 388 403 .59 1.694 1.519 1.945 1.503 2.474 52 277 1.679 .91 90 3950 7040 31 40 274 283 0 266 38 227 1.578 265 226 .634 1.415 .658 .501
18 61 80 51 51 9 29 57 80 51 52 5 29 0 0 13 14 8 17 50 83 25 25 38 34 .31 3.222 5.8 3.183 3.018 2.456 12 68 7.849 .14 40 4120 7030 33 37 294 298 0 75 48 27 3.002 75 27 .333 5.403 1.586 2.434
19 450 692 63 53 386 639 470 696 66 56 407 643 0 0 143 132 19 20 96 100 94 100 1025 1050 .604 1.655 1.58 1.948 1.544 2.673 52 300 1.598 .91 90 4250 7040 31 40 304 313 0 645 49 595 1.542 648 599 .648 1.472 .625 .557
20 1692 10381 62 45 1630 10335 1853 11506 65 48 1790 11460 0 0 426 2848 17 15 100 100 100 100 11965 13250 .158 6.34 6.402 6.234 6.248 1.566 52 318 6.848 .94 90 4410 7030 30 39 320 329 0 9670 42 9627 5.906 10718 10675 .169 5.964 2.562 2.576

Total number of rows: 44544

Table truncated, full table size 9287 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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