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Sample GSM989752 Query DataSets for GSM989752
Status Public on Aug 23, 2012
Title PC 582T
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 582T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 625T
disease free survival: 20.97
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/2008-08/81164.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 15137 10058 75 71 15062 9987 17534 11520 79 84 17458 11448 0 0 5792 4012 26 73 100 98 100 98 25049 28906 1.508 .663 .656 .605 .668 1.758 52 374 .658 .96 90 1810 7390 62 71 28 37 0 8490 60 8430 .56 9724 9663 1.787 .554 -.837 -.853
2 13895 9971 86 81 13808 9889 16676 11381 93 93 16590 11300 0 0 5682 3122 33 57 100 100 100 100 23697 27890 1.396 .716 .681 .805 .713 1.632 52 253 .676 .96 80 1960 7400 64 72 44 52 0 8416 68 8347 .605 9607 9538 1.654 .575 -.726 -.799
3 15791 42663 94 80 15696 42582 18656 46863 101 93 18561 46782 0 0 5992 11130 40 72 100 100 100 100 58278 65343 .369 2.713 2.52 3.202 2.592 1.931 52 285 2.647 .97 90 2120 7400 63 72 59 68 0 36011 68 35943 2.29 39556 39488 .437 2.127 1.195 1.089
4 13098 7947 90 93 13008 7854 17275 9972 106 117 17185 9878 0 0 7892 5200 122 123 88 78 84 76 20862 27063 1.656 .604 .575 .489 .625 2.734 52 313 .616 .97 90 2270 7390 62 71 74 83 0 6708 79 6629 .51 8417 8338 1.962 .485 -.972 -1.043
5 1151 258 86 81 1064 177 1169 252 91 96 1082 171 0 0 158 100 36 60 100 87 100 62 1241 1253 6.011 .166 .158 .143 .161 1.917 32 217 .153 .63 70 2420 7380 62 69 90 97 0 218 68 149 .14 213 144 7.122 .133 -2.832 -2.906
6 8692 14468 94 83 8598 14384 9744 16458 102 103 9649 16375 0 0 3892 7142 43 78 100 100 100 100 22982 26024 .598 1.673 1.697 1.74 1.615 2.007 80 336 1.753 .96 100 2570 7400 63 73 104 114 0 12212 70 12141 1.412 13892 13822 .708 1.432 .498 .519
7 253 137 80 80 172 56 255 140 87 95 174 59 0 0 54 68 32 76 100 25 100 6 228 233 3.071 .326 .339 .369 .413 2.285 32 220 1.137 .33 70 2720 7370 61 68 120 127 0 116 68 47 .275 118 50 3.639 .286 -1.863 -1.805
8 17597 40481 84 89 17513 40392 20220 42844 96 123 20135 42754 0 0 5918 8336 73 271 100 100 100 100 57905 62889 .434 2.306 2.123 2.55 2.189 1.554 52 293 2.246 .97 90 2870 7390 62 71 134 143 0 34170 75 34094 1.947 36164 36088 .514 1.792 .961 .842
9 107 113 83 86 24 26 100 104 86 100 17 17 0 0 36 51 29 61 40 19 17 3 50 34 .923 1.083 1 1.216 1.664 4.16 52 280 3.798 .35 90 3010 7380 61 70 148 157 -50 95 73 22 .914 88 14 1.094 .844 -.129 -.245
10 114 130 78 90 36 39 111 126 86 115 33 35 0 0 32 50 55 130 25 3 0 0 75 68 .923 1.083 1.061 1.293 .917 4.82 52 291 2.772 .82 90 3160 7380 61 70 163 172 -50 110 76 33 .914 106 30 1.094 .895 -.129 -.16
11 506 1026 78 92 428 934 590 1147 85 107 511 1055 0 0 228 420 32 79 88 94 84 90 1362 1566 .458 2.182 2.065 2.48 2.103 1.809 52 254 2.176 .94 80 3310 7380 62 70 179 187 0 866 78 788 1.842 968 891 .543 1.743 .881 .801
12 342 660 77 92 265 567 333 636 87 110 256 544 0 0 66 166 39 81 100 100 100 100 832 800 .467 2.14 2.125 2.118 2.061 1.419 52 282 2.471 .86 90 3470 7400 63 72 194 203 0 557 78 479 1.806 537 459 .554 1.794 .853 .843
13 266 172 78 94 187 77 273 174 86 111 195 79 0 0 86 74 31 71 92 51 86 19 264 274 2.429 .412 .405 .358 .467 3.233 52 269 .65 .41 80 3610 7380 62 70 209 217 0 145 79 65 .348 147 67 2.877 .342 -1.525 -1.548
14 199 211 82 94 116 117 198 205 91 122 115 111 0 0 40 71 39 114 100 50 81 9 233 226 .991 1.009 .965 .849 1.31 2.392 32 225 3.058 .46 70 3760 7370 61 68 224 231 0 178 79 99 .851 173 94 1.175 .815 -.232 -.296
15 81 79 77 82 4 -2 76 50 81 105 -1 -31 0 0 24 131 30 92 11 1 1 1 2 -32 null null null 2.592 2.738 3.571 52 318 4.407 .73 90 3910 7380 61 70 238 247 -50 67 69 -2 null 42 -26 null null null null
16 2427 1660 78 85 2349 1574 2571 1659 85 113 2493 1573 0 0 594 339 31 87 100 100 100 100 3923 4066 1.492 .67 .631 .691 .628 1.437 52 239 .644 .94 80 4060 7390 63 71 254 262 0 1401 72 1329 .566 1400 1328 1.768 .533 -.822 -.909
17 103 138 80 91 23 46 100 136 89 124 20 44 0 0 25 58 36 119 26 7 3 0 69 64 .5 2 2.2 2.624 2.109 3.931 52 291 6.806 .45 90 4210 7380 61 70 268 277 -50 116 77 39 1.688 115 37 .592 1.857 .755 .893
18 75 54 82 95 -7 -40 73 46 89 122 -9 -48 0 0 18 24 35 113 1 0 0 0 -47 -57 null null null 3.022 2.837 2.743 52 310 5.71 .48 90 4360 7370 60 69 283 292 -50 46 80 -34 null 39 -41 null null null null
19 421 405 77 88 343 317 420 402 87 120 342 314 0 0 81 106 40 129 100 94 100 73 660 656 1.082 .924 .918 .89 .895 1.516 52 252 1.161 .79 80 4520 7370 61 69 300 308 0 342 74 268 .78 339 265 1.282 .775 -.358 -.368
20 2118 6504 79 94 2038 6410 2330 6773 85 111 2250 6678 0 0 716 1682 30 75 100 100 100 100 8448 8928 .318 3.145 2.968 3.412 3.049 1.435 52 233 3.099 .97 80 4660 7390 63 71 314 322 0 5490 79 5411 2.655 5717 5637 .377 2.505 1.409 1.325

Total number of rows: 44544

Table truncated, full table size 9415 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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