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Sample GSM989674 Query DataSets for GSM989674
Status Public on Aug 23, 2012
Title PC 430T
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 430T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 69
pre-operation treatment: None
individual: PC 343T
disease free survival: 61.97
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/2008-08/81175.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 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 17768 12727 62 82 17706 12645 19552 13273 76 91 19489 13191 0 0 4740 3155 102 42 100 100 100 100 30351 32680 1.4 .714 .677 .718 .702 1.465 32 231 .681 .97 70 1890 7640 40 47 41 48 0 10730 69 10661 .602 11191 11122 1.661 .571 -.732 -.809
2 14941 10087 69 95 14871 9991 19403 12535 227 104 19333 12440 0 0 8074 5417 485 49 94 100 90 100 24862 31773 1.488 .672 .643 .745 .687 2.721 52 274 .665 .97 80 2040 7650 41 49 56 64 0 8505 80 8424 .566 10569 10488 1.765 .543 -.82 -.882
3 11526 16042 61 91 11464 15951 15275 20408 66 94 15213 20317 0 0 6287 8271 22 39 100 100 100 100 27415 35530 .719 1.391 1.336 1.552 1.37 2.419 52 282 1.374 .97 80 2190 7650 41 49 71 79 0 13525 77 13449 1.173 17207 17130 .852 1.126 .23 .171
4 15025 9645 61 90 14964 9555 19952 12388 65 92 19891 12298 0 0 8322 5363 21 39 100 100 98 100 24519 32189 1.566 .639 .618 .776 .653 3.02 52 259 .635 .97 80 2350 7640 40 48 87 95 0 8132 76 8056 .538 10445 10369 1.857 .521 -.893 -.94
5 640 226 65 92 575 133 728 237 69 94 663 144 0 0 237 78 21 40 98 84 98 73 708 807 4.323 .231 .217 .222 .223 2.47 52 216 .231 .8 80 2500 7650 41 49 102 110 0 191 78 112 .195 200 121 5.128 .183 -2.358 -2.449
6 4161 3985 69 95 4092 3890 4722 4102 76 102 4653 4007 0 0 3097 2606 29 51 100 98 100 98 7982 8660 1.052 .951 .861 1.083 .962 2.593 52 315 .894 .94 90 2650 7640 39 48 116 125 0 3360 80 3280 .802 3459 3378 1.248 .726 -.319 -.462
7 227 139 63 83 163 55 226 119 67 88 162 35 0 0 52 60 20 37 100 46 100 31 218 197 2.964 .337 .216 .3 .261 3.149 32 226 .38 .43 70 2800 7640 40 47 132 139 0 117 70 46 .284 100 30 3.515 .182 -1.814 -2.457
8 13709 18819 61 82 13647 18736 14305 19475 66 90 14243 19393 0 0 2344 3157 33 41 100 100 100 100 32383 33636 .728 1.373 1.362 1.374 1.368 1.312 32 232 1.354 .98 70 2940 7640 40 47 146 153 0 15867 69 15797 1.158 16420 16351 .864 1.148 .211 .199
9 188 125 57 82 131 43 192 125 61 92 135 43 0 0 37 39 17 40 100 53 100 18 174 178 3.047 .328 .319 .354 .421 2.659 32 161 .266 .32 60 3100 7650 42 48 163 169 0 105 69 36 .277 105 36 3.613 .269 -1.853 -1.897
10 193 129 60 85 133 43 190 122 64 101 130 36 0 0 35 44 18 60 100 31 100 3 176 166 3.093 .323 .277 .246 .319 4.847 32 214 .431 .31 70 3250 7640 40 47 177 184 0 109 72 36 .273 103 30 3.669 .233 -1.875 -2.099
11 462 698 60 98 402 600 460 687 63 105 400 589 0 0 47 138 17 53 100 100 100 100 1002 989 .67 1.493 1.473 1.462 1.52 1.611 32 223 1.602 .93 70 3400 7640 40 47 192 199 0 589 83 506 1.258 579 497 .795 1.242 .332 .312
12 353 525 59 96 294 429 398 556 61 106 339 459 0 0 124 187 16 61 96 94 94 94 723 798 .685 1.459 1.354 1.451 1.479 2.045 52 298 1.514 .9 80 3550 7640 40 48 207 215 0 443 81 362 1.23 469 387 .813 1.142 .299 .191
13 342 231 58 104 284 127 346 208 61 109 288 103 0 0 50 86 15 46 100 90 100 56 411 391 2.236 .447 .358 .354 .402 2.787 32 213 .521 .66 70 3700 7640 40 47 222 229 0 195 88 107 .377 175 87 2.652 .302 -1.407 -1.73
14 158 118 60 98 98 20 160 118 65 106 100 20 0 0 32 40 32 61 96 9 87 3 118 120 4.9 .204 .2 .316 .344 3.24 32 202 .9 .41 70 3850 7640 40 47 237 244 0 99 83 17 .172 99 17 5.812 .169 -2.539 -2.568
15 65 80 61 92 4 -12 63 72 64 99 2 -20 0 0 13 45 28 46 3 7 0 3 -8 -18 null null null 3.995 4.499 5.173 80 346 25.782 .09 100 4000 7640 39 49 251 261 -50 67 78 -10 null 61 -17 null null null null
16 845 859 57 86 787 772 1000 873 61 91 943 786 0 0 367 340 16 36 100 100 98 100 1559 1729 1.019 .981 .834 1.038 .964 2.596 52 206 .953 .93 80 4150 7640 40 48 267 275 0 724 73 651 .827 736 663 1.209 .703 -.274 -.509
17 82 125 56 79 26 46 71 113 59 85 15 34 0 0 36 67 16 46 48 35 38 16 72 49 .565 1.769 2.267 1.558 1.61 5.133 80 290 3.634 .43 100 4300 7630 38 48 281 291 -50 105 67 39 1.492 95 29 .67 1.911 .577 .934
18 60 67 56 84 3 -16 59 61 60 91 2 -23 0 0 14 34 18 56 15 6 2 0 -13 -21 null null null 2.457 2.483 3.102 80 314 9.793 .26 100 4450 7630 38 48 296 306 -50 56 71 -13 null 51 -19 null null null null
19 375 303 60 90 314 212 381 313 65 103 321 222 0 0 86 85 23 69 100 93 96 81 526 543 1.481 .675 .692 .649 .668 2.221 32 209 .853 .74 70 4600 7630 39 46 312 319 0 255 76 179 .569 264 187 1.757 .583 -.813 -.778
20 1830 7326 61 92 1769 7234 2299 9469 67 100 2238 9376 0 0 986 3756 35 49 96 100 96 100 9003 11614 .245 4.089 4.189 4.786 4.06 2.544 52 249 4.104 .97 80 4750 7640 40 48 327 335 0 6177 78 6099 3.448 7984 7905 .29 3.532 1.786 1.821

Total number of rows: 44544

Table truncated, full table size 9480 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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