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Sample GSM989807 Query DataSets for GSM989807
Status Public on Aug 23, 2012
Title PC 498T
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 498T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 48
pre-operation treatment: None
individual: PC 551T
disease free survival: 22.83
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/2008-08/81180.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 11860 9733 48 72 11812 9660 13540 11168 51 79 13491 11096 0 0 4016 3601 15 33 100 100 100 100 21472 24587 1.223 .818 .822 .768 .806 2.507 52 364 .828 .99 90 1680 7700 17 26 35 44 0 9282 69 9213 .78 10651 10582 1.282 .784 -.359 -.35
2 12541 10547 48 61 12493 10486 14883 12729 51 67 14835 12668 0 0 4962 4201 15 26 100 100 100 100 22979 27503 1.191 .839 .854 .797 .822 2.806 52 262 .835 .99 80 1830 7700 18 26 51 59 0 10059 58 10001 .8 12140 12082 1.249 .814 -.321 -.296
3 14632 28256 43 61 14588 28195 17043 33431 48 69 16999 33370 0 0 5260 10567 15 33 100 100 100 100 42783 50369 .517 1.933 1.963 1.855 1.892 2.496 52 292 1.955 .99 90 1980 7700 17 26 65 74 0 26948 58 26890 1.843 31884 31825 .543 1.872 .882 .905
4 10341 8501 43 61 10298 8440 14267 10774 46 69 14223 10713 0 0 6952 5593 14 38 100 100 100 97 18738 24936 1.22 .82 .753 .867 .817 3.098 80 372 .81 .99 100 2140 7700 17 27 81 91 0 8107 58 8049 .782 10275 10217 1.279 .718 -.355 -.477
5 752 285 43 59 708 226 805 282 46 66 761 223 0 0 181 76 12 36 100 98 100 98 934 984 3.133 .319 .293 .313 .295 2.836 52 226 .311 .91 90 2290 7700 17 26 96 105 0 272 56 216 .304 269 213 3.285 .279 -1.716 -1.839
6 3882 4594 57 73 3824 4520 1761 2912 67 81 1704 2838 0 0 3662 4225 33 40 100 100 98 97 8344 4542 .846 1.182 1.665 1.1 1.135 2.81 120 504 1.162 .99 130 2440 7690 14 27 109 122 0 4381 70 4311 1.127 2777 2707 .887 1.588 .173 .668
7 206 160 52 67 154 92 217 160 63 76 164 92 0 0 52 40 33 40 92 90 88 59 246 256 1.674 .597 .561 .608 .609 3.141 52 227 .595 .8 80 2590 7690 17 25 127 135 0 153 64 88 .57 153 88 1.755 .535 -.812 -.902
8 16181 31666 46 62 16134 31603 18234 35494 51 69 18188 35432 0 0 4841 8350 25 37 100 100 100 100 47737 53620 .511 1.959 1.948 2.03 1.929 2.396 52 301 1.937 .99 90 2740 7690 16 25 141 150 0 30200 59 30140 1.868 33851 33792 .535 1.858 .902 .894
9 188 188 41 56 147 131 191 185 46 65 149 128 0 0 53 44 18 29 98 98 96 98 278 277 1.122 .891 .859 .923 .906 3.063 52 240 .844 .88 80 2900 7690 17 25 158 166 0 179 53 125 .85 176 122 1.177 .819 -.235 -.288
10 175 181 39 52 135 128 186 183 41 58 147 130 0 0 50 56 9 20 98 98 98 92 263 277 1.055 .948 .884 .941 .969 3.238 52 202 .944 .9 80 3050 7690 17 25 173 181 0 173 50 122 .904 175 124 1.106 .843 -.145 -.246
11 647 1105 40 52 607 1052 682 1141 43 63 642 1088 0 0 147 256 16 62 100 100 100 100 1659 1730 .577 1.733 1.695 1.737 1.746 2.255 52 235 1.715 .98 80 3190 7690 17 25 187 195 0 1054 50 1003 1.653 1088 1038 .605 1.616 .725 .693
12 664 1500 41 56 622 1443 691 1544 46 66 649 1487 0 0 129 250 17 61 100 100 100 100 2065 2136 .431 2.32 2.291 2.342 2.291 2.197 52 253 2.308 .99 80 3350 7690 17 25 203 211 0 1431 53 1376 2.213 1473 1418 .452 2.185 1.146 1.128
13 363 281 38 52 325 228 382 277 41 59 344 224 0 0 98 69 10 23 100 100 100 96 553 568 1.425 .702 .651 .717 .705 2.973 52 300 .661 .93 90 3500 7680 15 24 217 226 0 268 50 217 .669 264 214 1.495 .621 -.58 -.687
14 145 177 39 55 106 122 151 177 43 62 111 122 0 0 34 45 12 29 100 98 98 90 228 233 .869 1.151 1.099 1.134 1.108 2.715 52 223 1.165 .86 80 3650 7690 17 25 233 241 0 169 52 116 1.098 169 116 .911 1.048 .134 .068
15 44 48 38 52 5 -4 42 44 43 59 3 -8 0 0 8 18 15 29 10 5 2 1 1 -5 null null null 2.74 3.461 6.931 80 320 2.794 .45 100 3800 7680 15 25 247 257 -50 46 50 -4 null 42 -8 null null null null
16 935 1254 41 61 894 1193 1019 1338 46 73 978 1277 0 0 274 321 23 49 100 100 100 100 2087 2255 .749 1.334 1.306 1.379 1.301 2.572 52 227 1.301 .98 80 3950 7680 16 24 263 271 0 1196 58 1138 1.273 1276 1218 .786 1.245 .348 .316
17 111 180 43 61 68 119 117 188 48 81 74 127 0 0 24 47 24 91 92 69 76 5 187 201 .571 1.75 1.716 1.735 1.832 3.015 52 228 1.856 .82 80 4100 7680 16 24 278 286 0 172 58 113 1.669 179 121 .599 1.637 .739 .711
18 41 45 42 62 -1 -16 40 41 49 76 -2 -20 0 0 5 12 20 81 0 0 0 0 -17 -22 null null null 4.359 4.423 6.778 80 320 3.74 .62 100 4250 7680 15 25 292 302 -50 43 59 -15 null 39 -19 null null null null
19 560 571 43 61 516 510 565 578 49 70 521 517 0 0 116 144 21 48 100 100 100 100 1026 1038 1.012 .988 .992 .968 .96 2.4 52 251 .987 .97 80 4400 7680 16 24 308 316 0 545 58 486 .943 551 493 1.061 .946 -.085 -.079
20 2654 11645 43 65 2610 11580 2907 12629 49 74 2863 12564 0 0 723 2760 20 44 100 100 100 100 14190 15427 .225 4.437 4.388 4.552 4.408 2.296 52 240 4.414 .99 80 4560 7680 16 24 324 332 0 11106 62 11044 4.231 12044 11982 .236 4.185 2.081 2.065

Total number of rows: 44544

Table truncated, full table size 9304 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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