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Sample GSM989793 Query DataSets for GSM989793
Status Public on Aug 23, 2012
Title PC 482T
Sample type RNA
 
Channel 1
Source name Human 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 482T
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 65
pre-operation treatment: None
individual: PC 494T
disease free survival: 41.43
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/2008-08/80937.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 14690 9282 138 160 14552 9122 18584 11049 147 187 18446 10889 0 0 6943 3411 57 110 100 100 100 100 23674 29335 1.595 .627 .59 .758 .611 2.198 52 305 .585 .96 80 1700 8290 25 33 34 42 0 13429 231 13197 .907 15985 15753 1.103 .854 -.141 -.228
2 13884 8272 125 149 13759 8123 18525 10494 139 175 18400 10345 0 0 7267 3948 62 106 100 100 94 100 21882 28745 1.694 .59 .562 .761 .593 2.675 52 254 .568 .97 80 1850 8290 25 33 49 57 0 11967 216 11752 .854 15182 14966 1.171 .813 -.227 -.298
3 12567 13310 130 161 12437 13149 16104 16400 149 191 15974 16239 0 0 6260 5581 65 128 100 100 98 100 25586 32213 .946 1.057 1.017 1.347 1.025 2.424 52 264 1.018 .97 80 2000 8290 25 33 64 72 0 19256 233 19023 1.53 23726 23493 .654 1.471 .613 .557
4 18450 10518 137 164 18313 10354 19321 11162 149 185 19184 10998 0 0 3233 2216 55 100 100 100 100 100 28667 30182 1.769 .565 .573 .557 .579 1.385 32 214 .579 .95 70 2150 8280 24 31 79 86 0 15217 237 14979 .818 16148 15911 1.223 .829 -.29 -.27
5 978 245 134 154 844 91 964 233 154 175 830 79 0 0 155 71 187 131 100 21 100 6 935 909 9.275 .108 .095 .097 .105 2.165 32 208 .135 .45 70 2300 8280 24 31 94 101 0 354 223 132 .156 337 114 6.411 .138 -2.681 -2.86
6 9085 8708 161 177 8924 8531 9983 9355 202 204 9822 9178 0 0 3048 2822 133 121 100 100 100 100 17455 19000 1.046 .956 .934 .942 .95 1.627 52 327 .954 .97 90 2450 8280 23 32 108 117 0 12598 256 12342 1.383 13534 13278 .723 1.352 .468 .435
7 367 199 144 165 223 34 354 167 179 200 210 2 0 0 109 108 99 128 83 16 66 8 257 212 6.559 .152 .01 .189 .144 6.792 12 68 .125 .14 40 2590 8270 25 29 125 129 0 288 239 49 .221 242 3 4.534 .014 -2.181 -6.181
8 13566 14521 130 163 13436 14358 16704 16420 145 184 16574 16257 0 0 7158 6079 65 100 100 100 100 100 27794 32831 .936 1.069 .981 1.295 1.026 2.352 52 227 1.013 .95 80 2750 8280 24 32 139 147 0 21008 236 20772 1.546 23755 23519 .647 1.419 .629 .505
9 168 150 113 136 55 14 155 147 129 152 42 11 0 0 65 72 66 79 36 17 13 3 69 53 3.929 .255 .262 1.02 1.194 3.425 80 340 2.152 .3 100 2890 8280 23 33 152 162 -50 217 197 20 .368 213 16 2.715 .379 -1.441 -1.4
10 226 234 112 128 114 106 228 222 127 143 116 94 0 0 45 68 48 78 91 58 66 33 220 210 1.075 .93 .81 1.048 1.122 1.89 12 104 1.659 .52 50 3040 8280 25 30 169 174 0 339 185 153 1.345 321 136 .743 1.172 .428 .229
11 448 692 110 128 338 564 480 711 123 151 370 583 0 0 159 224 52 97 94 98 88 92 902 953 .599 1.669 1.576 1.739 1.655 1.9 52 269 1.687 .84 80 3200 8280 24 32 184 192 0 1001 185 816 2.414 1029 843 .414 2.28 1.271 1.189
12 634 779 113 134 521 645 637 796 124 145 524 662 0 0 138 172 52 73 100 100 100 100 1166 1186 .808 1.238 1.263 1.234 1.218 1.416 32 201 1.302 .89 70 3350 8280 24 31 199 206 0 1127 194 933 1.791 1152 958 .558 1.828 .841 .87
13 333 244 116 135 217 109 347 248 132 156 231 113 0 0 131 88 111 106 75 55 53 11 326 344 1.991 .502 .489 .602 .544 2.735 52 244 .588 .71 80 3500 8280 24 32 214 222 0 353 195 158 .727 359 163 1.376 .708 -.461 -.499
14 245 220 110 129 135 91 243 204 122 157 133 75 0 0 57 51 50 114 91 41 75 0 226 208 1.484 .674 .564 .644 .663 2.693 12 104 2.14 .29 50 3660 8270 24 29 231 236 0 318 187 132 .975 295 109 1.025 .816 -.036 -.294
15 114 105 120 143 -6 -38 108 81 135 163 -12 -62 0 0 44 89 59 100 6 6 3 2 -44 -74 null null null 2.399 2.662 3.494 80 345 2.507 .5 100 3800 8270 22 32 243 253 -50 152 207 -55 null 117 -90 null null null null
16 1384 1193 119 153 1265 1040 1472 1233 131 166 1353 1080 0 0 356 252 55 80 100 100 100 100 2305 2433 1.216 .822 .798 .843 .852 1.417 32 190 .815 .91 70 3950 8270 23 30 259 266 0 1726 221 1505 1.189 1784 1562 .841 1.155 .25 .208
17 150 173 119 140 31 33 136 150 137 160 17 10 0 0 80 133 69 144 15 10 5 5 64 27 .939 1.065 .588 1.454 1.519 4.484 80 296 2.1 .4 100 4100 8270 22 32 273 283 -50 250 203 48 1.54 217 14 .649 .851 .623 -.233
18 111 96 117 146 -6 -50 99 86 135 169 -18 -60 0 0 40 53 96 163 3 0 0 0 -56 -78 null null null 2.51 2.223 3.033 80 302 3.868 .44 100 4250 8260 21 31 288 298 -50 139 211 -72 null 124 -87 null null null null
19 621 478 105 134 516 344 643 474 126 153 538 340 0 0 231 157 103 113 96 92 90 80 860 878 1.5 .667 .632 .679 .654 1.595 52 240 .658 .87 80 4410 8270 23 31 305 313 0 692 194 498 .964 686 492 1.037 .914 -.052 -.129
20 2645 5944 103 122 2542 5822 3383 7260 120 134 3280 7138 0 0 1250 2648 61 70 100 100 100 98 8364 10418 .437 2.29 2.176 2.221 2.26 1.987 52 243 2.321 .96 80 4560 8270 23 31 320 328 0 8599 177 8423 3.313 10503 10327 .302 3.148 1.728 1.655

Total number of rows: 44544

Table truncated, full table size 9863 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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