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Sample GSM989678 Query DataSets for GSM989678
Status Public on Aug 23, 2012
Title PC 339T
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 339T2.0
Organism Homo sapiens
Characteristics individual: PC 339T
disease state: Tumor
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/2008-08/81247.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 5368 6240 70 134 5298 6106 5841 7054 77 165 5771 6920 0 0 1578 2209 54 126 100 98 100 96 11404 12691 .868 1.153 1.199 1.056 1.193 3.804 80 417 1.153 .96 100 1790 6660 25 35 10 20 0 6315 136 6179 1.166 7139 7003 .857 1.213 .222 .279
2 5550 6608 73 123 5477 6484 5766 6703 78 134 5693 6579 0 0 1061 1096 31 75 100 100 100 100 11961 12272 .845 1.184 1.156 1.201 1.208 2.561 52 252 1.154 .97 90 1930 6660 25 34 24 33 0 6687 124 6562 1.198 6783 6658 .835 1.169 .261 .226
3 8225 5199 74 113 8151 5086 9099 5923 79 130 9025 5809 0 0 2861 2015 31 72 100 95 98 95 13237 14834 1.603 .624 .644 .556 .634 3.416 80 318 .61 .96 100 2100 6660 25 35 41 51 0 5261 114 5147 .631 5994 5879 1.584 .651 -.663 -.618
4 5970 6948 69 113 5901 6835 6083 7192 77 127 6014 7079 0 0 1155 1728 47 83 100 100 100 100 12736 13093 .863 1.158 1.177 1.128 1.173 2.888 80 316 1.155 .96 100 2240 6660 25 35 55 65 0 7031 114 6917 1.172 7278 7164 .853 1.191 .229 .252
5 340 129 66 107 274 21 353 120 71 123 286 12 0 0 93 75 44 79 97 21 96 3 295 298 13.048 .077 .042 .173 .206 8.847 80 352 .099 .15 100 2390 6660 25 35 70 80 0 131 108 21 .078 121 12 12.893 .042 -3.689 -4.558
6 120 214 71 104 49 109 78 175 83 154 7 70 0 0 145 174 47 208 16 8 8 8 158 77 .45 2.224 10 6.785 5.391 10.006 12 42 1.247 .69 50 2470 6700 31 36 80 85 0 217 105 110 2.251 177 71 .444 10.12 1.171 3.339
7 133 150 66 99 66 51 134 141 72 110 67 42 0 0 35 76 25 65 90 40 68 18 117 109 1.294 .773 .627 .833 1.09 8.379 32 212 -1 -1 70 2700 6650 25 32 102 109 0 152 100 52 .782 143 43 1.279 .634 -.355 -.657
8 7412 4507 69 107 7343 4399 8122 4843 83 121 8052 4735 0 0 2203 1458 122 83 96 98 96 97 11742 12787 1.669 .599 .588 .629 .601 3.186 80 353 .59 .97 100 2840 6660 25 35 115 125 0 4561 108 4452 .606 4901 4792 1.649 .595 -.722 -.749
9 131 131 63 95 67 36 130 113 87 113 66 18 0 0 51 86 155 89 5 23 0 7 103 84 1.861 .537 .273 1.671 .972 10.787 52 216 .262 .09 80 2980 6670 27 35 130 138 0 133 96 36 .544 114 18 1.839 .276 -.879 -1.857
10 144 266 57 102 86 164 141 246 63 110 83 144 0 0 50 127 24 58 86 82 78 58 250 227 .524 1.907 1.735 1.889 1.94 5.832 80 264 2.598 .49 100 3140 6660 25 35 145 155 0 269 103 166 1.93 249 146 .518 1.756 .948 .812
11 439 625 55 89 384 536 434 602 59 104 378 513 0 0 128 229 21 58 97 98 97 95 920 891 .716 1.396 1.357 1.391 1.358 3.285 80 260 1.4 .88 100 3290 6660 25 35 160 170 0 632 90 542 1.413 609 519 .708 1.373 .498 .458
12 321 581 54 95 266 486 310 561 59 104 255 466 0 0 105 204 22 58 98 98 97 97 752 721 .547 1.827 1.827 1.776 1.815 3.444 80 313 1.904 .82 110 3440 6660 24 35 174 185 0 588 96 492 1.849 568 472 .541 1.849 .887 .887
13 272 232 57 104 215 127 243 215 62 117 186 110 0 0 212 143 23 75 97 62 96 37 342 296 1.693 .591 .591 .588 .637 5.812 80 397 .671 .63 110 3590 6660 24 35 189 200 0 235 105 129 .598 218 111 1.673 .598 -.742 -.741
14 212 275 62 103 150 171 178 182 65 114 115 79 0 0 286 509 24 66 100 56 93 30 321 194 .877 1.14 .687 .771 .965 6.254 80 354 .201 .25 100 3750 6660 25 35 206 216 0 278 104 173 1.154 184 80 .867 .695 .206 -.525
15 119 68 81 93 38 -25 130 62 90 123 49 -31 0 0 40 46 44 103 50 0 0 0 13 18 null null null .926 1.059 5.463 12 54 -1 -1 40 3900 6690 31 35 224 228 0 69 94 -25 null 63 -31 null null null null
16 970 791 73 116 897 675 962 713 78 133 889 597 0 0 276 543 31 197 100 95 100 80 1572 1486 1.329 .753 .672 .684 .672 3.464 80 488 .768 .73 110 4050 6660 24 35 235 246 0 800 117 683 .762 722 604 1.313 .68 -.393 -.557
17 124 161 69 133 55 28 110 131 74 146 41 -1 0 0 46 117 27 72 73 21 42 7 83 40 1.964 .509 null 1.389 1.271 5.489 52 302 2.882 .19 90 4210 6640 23 32 252 261 0 163 135 28 .515 133 -1 1.941 null -.957 null
18 78 85 77 140 1 -55 76 69 97 178 -1 -70 0 0 30 60 210 378 0 0 0 0 -54 -71 null null null 3.633 4.556 6.194 120 496 9.224 .18 120 4350 6650 23 35 265 277 -50 86 142 -56 null 70 -71 null null null null
19 400 370 82 157 317 212 387 347 86 167 304 190 0 0 94 147 33 92 100 83 100 56 529 494 1.495 .669 .625 .619 .697 3.955 80 374 .699 .6 110 4500 6660 24 35 280 291 0 374 159 215 .677 351 192 1.478 .632 -.563 -.661
20 2091 5311 70 151 2021 5159 1950 5320 80 173 1879 5168 0 0 1185 2110 41 102 100 100 100 100 7180 7047 .392 2.553 2.75 2.536 2.768 3.023 80 331 2.392 .94 110 4650 6650 23 34 295 306 0 5375 153 5221 2.583 5384 5230 .387 2.783 1.369 1.477

Total number of rows: 44544

Table truncated, full table size 9496 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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