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Sample GSM989712 Query DataSets for GSM989712
Status Public on Aug 23, 2012
Title PC 336T
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 336T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 56
pre-operation treatment: None
individual: PC 45T
disease free survival: 91.77
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/2008-09/81275.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 7906 6962 49 197 7857 6764 8809 8097 52 209 8760 7900 0 0 2921 3170 20 105 100 96 100 92 14621 16660 1.162 .861 .902 .766 .884 5.18 80 332 .866 .95 100 1760 7060 24 34 4 14 0 6316 179 6136 .781 7345 7167 1.28 .818 -.357 -.29
2 6739 5924 50 197 6688 5727 8368 7171 56 220 8317 6974 0 0 3559 3430 22 113 98 92 98 91 12415 15291 1.168 .856 .839 .747 .865 5.465 80 292 .859 .96 100 1900 7060 24 34 18 28 0 5374 179 5195 .777 6505 6327 1.287 .761 -.364 -.395
3 7468 11987 54 212 7414 11774 10192 16252 58 231 10138 16039 0 0 4655 8209 22 107 95 92 92 89 19188 26177 .63 1.588 1.582 1.471 1.645 5.121 120 398 1.637 .97 120 2050 7070 24 36 32 44 0 10874 192 10681 1.441 14743 14550 .694 1.435 .527 .521
4 8331 7582 54 208 8276 7373 8794 8139 62 223 8739 7930 0 0 2050 2445 67 110 100 98 100 98 15649 16669 1.122 .891 .907 .797 .886 4.169 80 406 .89 .96 110 2200 7050 22 33 47 58 0 6878 189 6689 .808 7383 7194 1.237 .823 -.307 -.281
5 482 209 60 212 421 -3 487 194 86 232 426 -18 0 0 131 117 262 214 92 5 21 0 418 408 null null null .2 .228 11.45 80 448 -.014 -.03 110 2350 7060 23 34 62 73 0 190 192 -3 null 176 -16 null null null null
6 6354 5386 67 252 6286 5133 6266 5389 82 258 6198 5136 0 0 863 908 51 127 100 100 100 100 11419 11334 1.225 .817 .829 .812 .823 2.669 80 345 .792 .97 110 2500 7060 23 34 77 88 0 4886 229 4656 .741 4889 4659 1.35 .752 -.433 -.412
7 156 205 58 247 97 -42 150 185 72 260 92 -62 0 0 75 119 47 117 68 8 48 1 55 30 null null null 1.36 1.363 18.331 120 398 -.277 -.05 120 2650 7050 22 34 92 104 0 186 224 -38 null 168 -56 null null null null
8 11416 18389 54 224 11362 18164 12365 20870 63 243 12310 20645 0 0 3959 7017 35 117 98 97 98 97 29526 32955 .626 1.599 1.677 1.575 1.633 3.812 80 399 1.601 .97 110 2810 7050 22 33 108 119 0 16682 203 16478 1.45 18933 18729 .69 1.521 .536 .605
9 169 131 58 195 111 -64 161 113 75 226 102 -82 0 0 45 70 48 119 93 0 59 0 47 20 null null null .606 .537 4.877 32 147 -.834 -.33 70 2970 7080 27 34 126 133 0 119 177 -58 null 103 -74 null null null null
10 160 232 49 206 111 26 160 218 54 229 111 12 0 0 47 113 22 117 96 16 92 5 137 123 4.269 .234 .108 .597 .692 9.284 80 291 -1 -1 100 3110 7060 24 34 139 149 0 210 187 24 .212 198 11 4.706 .098 -2.235 -3.35
11 530 856 48 208 481 648 531 832 52 231 482 624 0 0 135 252 19 119 100 100 100 95 1129 1106 .742 1.347 1.295 1.282 1.367 3.879 80 338 1.259 .81 110 3260 7060 23 34 153 164 0 777 189 588 1.222 755 566 .818 1.174 .289 .232
12 460 1046 48 209 412 837 456 993 50 227 408 783 0 0 109 348 18 111 100 100 100 100 1249 1191 .492 2.032 1.919 1.934 2.006 3.782 80 338 2.087 .83 110 3410 7060 23 34 168 179 0 949 190 759 1.843 901 710 .543 1.741 .882 .8
13 281 246 45 198 235 47 277 217 49 214 231 18 0 0 75 139 18 102 98 28 98 10 282 249 5 .2 .078 .387 .423 6.352 80 263 .172 .13 100 3560 7060 24 34 184 194 0 223 180 43 .181 197 16 5.512 .071 -2.462 -3.822
14 163 260 47 208 115 52 160 243 50 221 113 35 0 0 45 125 18 104 100 28 98 11 167 148 2.212 .452 .31 .845 1.097 7.337 80 216 -1 -1 100 3710 7060 24 34 199 209 0 236 189 47 .41 220 32 2.438 .281 -1.286 -1.831
15 79 102 46 226 33 -123 77 85 49 249 30 -140 0 0 28 79 16 125 73 0 45 0 -90 -110 null null null 5.845 6.585 9.717 120 371 -11.448 -.34 120 3860 7050 22 34 213 225 -100 93 205 -112 null 77 -127 null null null null
16 1065 1317 46 212 1019 1104 1076 1319 49 232 1029 1106 0 0 222 312 15 114 100 100 100 100 2123 2135 .923 1.083 1.075 1.071 1.065 3.176 80 279 1.005 .9 110 4010 7050 22 33 228 239 0 1195 192 1002 .983 1197 1003 1.017 .975 -.025 -.036
17 121 163 47 227 74 -64 126 130 50 238 79 -97 0 0 52 119 16 108 82 7 75 2 10 -18 null null null 2.014 1.842 17.549 120 308 -2.745 -.31 120 4160 7050 22 34 243 255 -50 148 206 -58 null 118 -88 null null null null
18 64 113 47 241 16 -128 56 78 50 263 9 -163 0 0 24 97 16 128 35 3 20 0 -112 -154 null null null 13.932 14.053 9.014 120 302 -22.652 -.24 120 4310 7050 22 34 258 270 -100 103 219 -116 null 71 -148 null null null null
19 396 515 46 212 349 302 381 468 48 240 335 255 0 0 86 198 15 110 100 88 100 58 651 590 1.156 .865 .761 .748 .752 4.53 80 256 .825 .63 110 4460 7050 22 33 273 284 0 467 192 274 .785 425 231 1.274 .691 -.349 -.534
20 1241 5370 47 223 1194 5147 1418 6137 50 247 1371 5914 0 0 556 2451 17 123 96 97 95 94 6341 7285 .232 4.311 4.314 4.496 4.401 4.041 120 367 4.463 .95 120 4610 7050 22 34 288 300 0 4871 202 4669 3.911 5567 5365 .256 3.913 1.967 1.968

Total number of rows: 44544

Table truncated, full table size 9681 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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