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Sample GSM989704 Query DataSets for GSM989704
Status Public on Aug 23, 2012
Title PC 494T
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 494T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 46
pre-operation treatment: None
individual: PC 540T
disease free survival: 18.30
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/2008-08/81142.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 GPL15973
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 33455 17780 120 164 33335 17616 38916 21096 126 173 38796 20931 0 0 13191 8162 52 59 100 100 100 100 50951 59727 1.892 .528 .54 .472 .53 1.633 52 313 .54 .98 80 2070 6910 35 43 67 75 0 16751 155 16596 .498 19875 19719 2.009 .508 -1.006 -.976
2 30756 16643 153 195 30603 16448 35629 20293 161 201 35475 20097 0 0 12138 7560 70 72 100 100 100 100 47051 55572 1.861 .537 .567 .49 .542 1.574 52 274 .547 .98 80 2220 6900 34 42 82 90 0 15680 184 15496 .506 19118 18934 1.975 .534 -.982 -.906
3 26671 34377 143 193 26527 34183 33265 42611 175 219 33121 42418 0 0 19677 25231 117 120 100 100 100 98 60710 75539 .776 1.289 1.281 1.293 1.266 1.809 80 287 1.289 .98 100 2380 6920 35 45 97 107 0 32387 182 32204 1.214 40145 39963 .824 1.207 .28 .271
4 37233 19997 170 191 37063 19806 38951 21116 219 243 38781 20925 0 0 9183 5442 137 154 100 100 100 100 56869 59706 1.871 .534 .54 .529 .536 1.329 52 239 .534 .98 90 2520 6910 34 43 111 120 0 18840 180 18660 .503 19894 19714 1.986 .508 -.99 -.976
5 1892 441 159 191 1732 250 2113 439 223 236 1953 248 0 0 646 125 171 142 100 80 98 36 1982 2201 6.928 .144 .127 .141 .152 2.485 52 237 .117 .68 80 2670 6910 35 43 127 135 0 415 180 236 .136 414 234 7.354 .12 -2.878 -3.063
6 13564 10166 319 323 13244 9843 14028 10874 397 362 13708 10551 0 0 6307 4484 283 224 100 100 100 100 23087 24259 1.346 .743 .77 .739 .731 1.657 52 300 .709 .95 90 2820 6900 33 42 141 150 0 9578 304 9273 .7 10245 9940 1.428 .725 -.514 -.464
7 476 226 208 235 268 -9 490 217 278 277 281 -17 0 0 158 96 234 171 63 3 5 0 259 264 null null null .258 .297 5.675 52 326 .576 .62 90 2970 6900 33 42 156 165 -50 213 221 -8 null 204 -16 null null null null
8 33513 43459 124 202 33388 43256 36015 48045 158 238 35890 47842 0 0 8890 12388 98 138 100 100 100 100 76644 83732 .772 1.296 1.333 1.285 1.308 1.351 52 270 1.311 .98 90 3130 6920 35 44 172 181 0 40944 190 40752 1.221 45264 45073 .819 1.256 .288 .329
9 153 242 100 156 52 85 143 245 125 198 43 88 0 0 40 82 87 135 15 25 1 3 137 131 .612 1.635 2.047 1.916 1.79 3.829 52 296 1.655 .69 90 3280 6900 33 42 187 196 -50 228 147 80 1.54 231 83 .649 1.928 .623 .947
10 185 319 87 146 98 172 171 307 100 184 84 160 0 0 53 84 72 245 65 15 18 0 270 244 .57 1.755 1.905 1.819 1.878 2.333 32 221 2.183 .65 70 3420 6890 33 40 202 209 0 301 138 162 1.654 289 151 .605 1.795 .726 .844
11 984 1242 86 149 898 1093 1106 1339 90 152 1019 1190 0 0 355 452 26 51 100 96 98 96 1991 2209 .822 1.217 1.168 1.228 1.231 1.728 52 312 1.233 .96 80 3580 6890 33 41 218 226 0 1170 140 1030 1.147 1261 1121 .872 1.1 .197 .138
12 644 1974 85 137 559 1836 617 2073 88 147 532 1936 0 0 146 480 25 52 100 100 100 100 2395 2468 .304 3.284 3.639 3.24 3.377 1.405 52 266 3.433 .96 80 3740 6890 33 41 234 242 0 1860 129 1730 3.094 1953 1824 .323 3.428 1.63 1.778
13 460 368 81 142 379 226 498 363 86 151 417 220 0 0 167 118 29 56 94 92 92 82 605 637 1.677 .596 .528 .611 .617 2.263 52 272 .577 .78 80 3880 6890 33 41 248 256 0 347 134 213 .562 342 207 1.78 .497 -.832 -1.009
14 244 273 81 143 162 130 239 285 87 154 158 141 0 0 51 51 25 62 100 87 100 59 292 299 1.246 .802 .892 .758 .794 2.179 32 222 .968 .61 70 4040 6900 34 41 264 271 0 257 135 122 .756 269 133 1.323 .841 -.404 -.25
15 96 88 80 143 16 -54 95 66 86 154 15 -77 0 0 30 89 25 54 28 3 5 1 -38 -62 null null null 3.195 3.447 2.951 52 291 6.891 .29 90 4190 6910 34 43 278 287 -50 83 135 -51 null 62 -73 null null null null
16 4012 2385 85 152 3927 2233 4179 2535 88 155 4093 2383 0 0 842 673 26 47 100 100 100 100 6160 6476 1.759 .569 .582 .542 .569 1.443 52 230 .578 .98 80 4340 6920 36 44 294 302 0 2247 143 2104 .536 2388 2245 1.867 .549 -.9 -.866
17 129 255 87 155 42 100 132 238 90 158 45 83 0 0 30 79 25 48 75 71 31 46 142 128 .42 2.381 1.844 2.311 2.095 5.641 32 212 6.522 .25 70 4490 6900 34 41 309 316 0 240 146 94 2.243 224 78 .446 1.738 1.166 .797
18 84 78 87 157 -3 -79 81 71 94 166 -6 -85 0 0 19 40 29 60 5 1 1 0 -82 -91 null null null 5.737 5.672 4.718 52 324 14.899 .12 90 4640 6890 32 41 323 332 -50 73 148 -74 null 67 -80 null null null null
19 843 626 95 161 748 465 847 591 101 168 752 430 0 0 188 162 34 59 100 100 100 100 1213 1182 1.609 .622 .572 .606 .57 1.657 52 280 .596 .86 80 4790 6890 33 41 339 347 0 590 152 438 .586 557 405 1.707 .539 -.772 -.892
20 4056 10327 96 169 3960 10158 4184 11272 98 173 4088 11103 0 0 810 2901 27 63 100 100 100 100 14118 15191 .39 2.565 2.716 2.464 2.644 1.379 52 251 2.677 .98 80 4950 6900 34 42 355 363 0 9729 159 9570 2.417 10620 10460 .414 2.559 1.273 1.355

Total number of rows: 44544

Table truncated, full table size 9798 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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