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Sample GSM989726 Query DataSets for GSM989726
Status Public on Aug 23, 2012
Title PC 339T2
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 339T2.1
Organism Homo sapiens
Characteristics disease state: Tumor
individual: PC 339T
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/2008-09/81281.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) [email protected]
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 11726 16594 81 192 11644 16402 11828 17068 88 200 11746 16875 0 0 1167 1900 64 84 100 100 100 100 28046 28621 .71 1.409 1.437 1.406 1.424 2.139 52 360 1.446 .97 90 1920 6710 30 39 31 40 0 14801 171 14630 1.256 15224 15052 .796 1.281 .329 .358
2 13640 19373 88 200 13552 19172 14012 19744 94 209 13924 19543 0 0 2071 3437 36 92 100 100 100 100 32724 33467 .707 1.415 1.404 1.407 1.422 2.275 52 297 1.401 .98 90 2060 6720 31 40 45 54 0 17280 178 17100 1.262 17611 17431 .792 1.252 .336 .324
3 18941 34137 81 191 18860 33946 21993 38990 88 199 21911 38799 0 0 8261 13910 35 91 100 100 98 100 52806 60710 .556 1.8 1.771 1.962 1.793 3.868 80 335 1.772 .98 100 2230 6710 30 40 62 72 0 30448 170 30278 1.605 34777 34607 .623 1.579 .683 .659
4 14881 20879 83 174 14798 20705 15049 20619 89 185 14965 20444 0 0 2088 3029 33 89 100 100 100 100 35503 35409 .715 1.399 1.366 1.397 1.393 2.274 80 276 1.392 .98 110 2370 6720 30 41 75 86 0 18623 155 18468 1.248 18391 18235 .801 1.219 .32 .285
5 842 340 89 193 753 146 840 323 106 222 750 130 0 0 195 116 67 130 100 48 98 16 899 880 5.158 .194 .173 .158 .192 5.621 80 320 .188 .51 110 2520 6720 30 41 90 101 0 303 172 130 .173 288 116 5.782 .155 -2.532 -2.693
6 11592 13764 112 240 11479 13523 11203 13683 145 271 11090 13442 0 0 1952 2496 95 149 100 100 100 100 25002 24532 .849 1.178 1.212 1.175 1.186 2.118 80 373 1.209 .98 110 2670 6710 29 40 105 116 0 12277 214 12062 1.051 12204 11990 .952 1.081 .071 .113
7 300 305 99 200 200 105 288 300 127 222 188 99 0 0 91 135 81 130 90 36 71 5 305 287 1.905 .525 .527 .586 .72 5.602 52 194 .408 .29 90 2820 6740 33 42 121 130 0 272 178 94 .468 268 88 2.136 .47 -1.095 -1.09
8 23619 41143 85 192 23533 40950 23777 40989 94 206 23691 40797 0 0 3316 5434 49 91 100 100 100 100 64483 64488 .575 1.74 1.722 1.741 1.758 2.089 80 359 1.762 .99 110 2970 6710 29 40 135 146 0 36697 171 36525 1.552 36560 36389 .644 1.536 .634 .619
9 248 263 80 171 167 91 227 267 87 186 146 95 0 0 82 114 39 87 97 51 90 21 258 241 1.835 .545 .651 .717 .767 5.55 80 315 .544 .33 110 3120 6710 29 40 150 161 0 235 153 81 .486 238 85 2.057 .58 -1.041 -.785
10 241 440 80 157 161 282 244 423 84 174 163 265 0 0 69 159 33 85 97 91 88 68 443 428 .571 1.752 1.626 1.656 1.889 3.966 80 261 2.055 .68 100 3270 6710 30 40 166 176 0 392 140 252 1.562 377 236 .64 1.45 .644 .536
11 732 1657 72 171 659 1485 819 1673 78 185 746 1502 0 0 393 855 28 95 90 93 89 90 2144 2248 .444 2.253 2.013 2.44 2.169 4.045 120 365 2.27 .94 120 3420 6710 29 41 180 192 0 1478 153 1325 2.01 1492 1340 .498 1.796 1.007 .845
12 712 1088 71 170 641 917 715 1066 75 181 643 895 0 0 176 272 27 91 100 100 100 100 1558 1538 .699 1.431 1.392 1.426 1.361 2.613 80 259 1.408 .91 100 3570 6710 30 40 196 206 0 970 152 818 1.276 951 798 .784 1.242 .352 .312
13 448 366 74 159 374 207 443 358 76 168 369 199 0 0 139 157 28 78 100 80 98 56 581 568 1.807 .553 .539 .514 .507 4.403 80 320 .531 .63 110 3720 6710 29 40 210 221 0 326 142 185 .494 319 177 2.026 .481 -1.018 -1.056
14 273 330 71 148 201 182 260 310 74 168 189 161 0 0 89 125 27 84 100 77 98 47 383 350 1.104 .905 .852 .774 .852 5.094 80 232 .809 .52 100 3870 6710 30 40 226 236 0 294 132 162 .808 277 144 1.238 .76 -.308 -.396
15 115 80 70 160 44 -80 111 62 75 174 41 -98 0 0 41 56 30 81 62 2 35 0 -36 -57 null null null 4.462 5.57 8.382 120 373 -1.759 -.29 120 4020 6700 28 40 240 252 -50 71 143 -71 null 55 -87 null null null null
16 1841 2381 70 159 1771 2222 1860 2341 75 173 1790 2181 0 0 380 555 29 80 100 100 100 100 3993 3971 .797 1.255 1.218 1.232 1.278 2.468 80 296 1.258 .96 110 4180 6700 28 39 256 267 0 2124 142 1982 1.119 2088 1945 .894 1.087 .162 .12
17 205 175 70 166 135 9 207 167 72 177 137 1 0 0 67 80 26 80 93 17 88 3 144 138 15 .067 .007 .424 .369 7.258 80 200 .144 .11 100 4330 6710 30 40 272 282 0 156 148 8 .059 149 1 16.817 .007 -4.072 -7.263
18 96 73 72 155 23 -81 86 62 75 167 14 -92 0 0 42 53 28 80 35 1 20 0 -58 -78 null null null 6.459 5.925 5.545 120 367 -4.298 -.24 120 4480 6700 28 40 286 298 -100 65 138 -72 null 55 -82 null null null null
19 725 951 74 160 651 790 700 894 81 173 626 733 0 0 194 339 35 84 100 100 100 100 1441 1359 .824 1.214 1.171 1.152 1.227 2.845 80 309 1.249 .9 110 4630 6700 28 39 301 312 0 848 143 705 1.082 797 654 .924 1.044 .114 .063
20 2741 14396 74 167 2666 14228 2689 14274 78 177 2615 14106 0 0 600 2651 33 88 100 100 100 100 16894 16721 .187 5.337 5.394 5.441 5.449 2.279 80 318 5.264 .98 110 4770 6700 28 39 315 326 0 12840 149 12691 4.76 12732 12582 .21 4.811 2.251 2.266

Total number of rows: 44544

Table truncated, full table size 9657 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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