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Sample GSM989695 Query DataSets for GSM989695
Status Public on Aug 23, 2012
Title PC 634T
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 634T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 389T
disease free survival: 40.83
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/2008-08/81087.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 11602 15746 89 70 11513 15675 13224 19215 93 82 13135 19144 0 0 4973 7294 32 57 100 100 100 100 27188 32279 .734 1.362 1.457 1.301 1.416 3.591 32 236 1.41 .88 70 1720 6830 35 42 28 35 0 13947 62 13884 1.206 17020 16957 .829 1.291 .27 .368
2 10407 14558 95 78 10311 14480 12258 15397 102 95 12162 15319 0 0 5694 8617 34 79 100 100 100 96 24791 27481 .712 1.404 1.26 1.257 1.445 4.067 32 230 1.464 .92 70 1880 6830 35 42 44 51 0 12895 69 12826 1.244 13638 13569 .804 1.116 .315 .158
3 12161 18350 103 71 12058 18278 12305 21983 109 91 12202 21911 0 0 7163 12046 59 71 100 90 100 87 30336 34113 .66 1.516 1.796 .799 1.491 8.202 32 232 1.611 .91 70 2020 6830 35 42 58 65 0 16254 63 16190 1.343 19472 19408 .745 1.591 .425 .67
4 13825 19771 99 70 13725 19700 15866 22626 103 82 15767 22555 0 0 4786 6599 36 49 100 100 100 100 33425 38322 .697 1.435 1.431 1.468 1.459 2.423 32 171 1.462 .9 60 2170 6830 36 42 74 80 0 17512 62 17450 1.271 20041 19978 .787 1.267 .346 .342
5 508 386 100 78 407 308 551 399 106 90 450 321 0 0 233 141 38 54 87 90 87 90 715 771 1.321 .757 .713 .86 .75 4.309 32 214 .6 .69 70 2320 6830 35 42 88 95 0 342 69 273 .67 353 284 1.492 .632 -.577 -.662
6 9538 14789 125 89 9412 14700 11556 18476 134 106 11430 18387 0 0 4286 7588 53 77 100 100 100 100 24112 29817 .64 1.562 1.609 1.606 1.666 3.463 52 287 1.655 .92 80 2480 6830 35 43 104 112 0 13100 79 13021 1.383 16365 16287 .723 1.425 .468 .511
7 238 168 112 78 125 90 230 166 117 98 118 88 0 0 53 70 38 74 91 50 83 16 215 206 1.389 .72 .746 .692 .856 3.343 12 68 .447 .15 40 2630 6820 36 40 121 125 0 149 69 80 .638 147 78 1.568 .661 -.649 -.598
8 16880 22814 92 76 16788 22738 19238 29616 101 89 19146 29540 0 0 6645 13062 39 59 100 100 100 100 39526 48686 .738 1.354 1.543 .886 1.474 3.957 32 232 1.51 .93 70 2780 6820 34 41 134 141 0 20208 67 20140 1.2 26233 26165 .834 1.367 .263 .451
9 162 173 91 73 71 100 161 181 96 92 69 108 0 0 60 88 35 68 68 56 50 37 171 177 .71 1.408 1.565 1.113 1.47 4.023 32 175 2.115 .5 60 2920 6820 35 41 149 155 0 153 65 89 1.248 160 96 .802 1.386 .319 .471
10 158 201 82 79 75 122 158 198 89 88 75 119 0 0 52 80 30 55 71 84 56 53 197 194 .615 1.627 1.587 1.764 2.004 3.622 32 235 2.439 .45 70 3080 6820 34 41 164 171 0 178 70 108 1.441 175 105 .694 1.405 .527 .491
11 530 1014 81 74 449 940 570 1068 88 92 489 994 0 0 223 404 33 118 96 100 96 90 1389 1483 .478 2.094 2.033 2.29 2.074 2.252 32 232 2.35 .83 70 3240 6820 34 41 180 187 0 898 66 833 1.854 946 880 .539 1.801 .891 .848
12 392 837 84 67 307 769 393 833 89 81 309 765 0 0 108 221 31 74 100 100 100 100 1076 1074 .399 2.505 2.476 2.586 2.543 1.998 32 218 2.795 .8 70 3380 6820 34 41 194 201 0 741 59 681 2.219 738 678 .451 2.193 1.15 1.133
13 229 231 93 80 135 151 234 230 96 94 141 150 0 0 96 111 38 71 80 76 67 53 286 291 .894 1.119 1.064 1.327 1.097 3.168 52 283 1.606 .47 80 3520 6820 34 42 208 216 0 205 71 134 .991 204 133 1.009 .942 -.013 -.086
14 239 215 89 71 149 143 236 176 94 96 147 104 0 0 76 128 35 94 96 53 87 25 292 251 1.042 .96 .707 .83 .797 3.375 32 173 1.506 .46 60 3680 6820 35 41 225 231 0 190 63 127 .85 156 92 1.176 .627 -.234 -.674
15 123 110 89 76 34 34 113 96 101 98 24 20 0 0 47 66 69 88 28 15 1 1 68 44 1 1 .833 .835 .926 4.32 52 335 4.334 .14 90 3830 6820 33 42 238 247 -50 97 67 30 .886 85 18 1.129 .738 -.175 -.438
16 2519 1617 93 84 2426 1532 2582 1717 97 97 2489 1632 0 0 432 395 31 53 100 100 100 100 3958 4121 1.584 .631 .656 .612 .655 1.724 32 168 .615 .92 60 3980 6820 35 41 255 261 0 1432 74 1357 .559 1521 1446 1.788 .581 -.838 -.784
17 182 271 88 82 94 189 183 265 94 96 94 182 0 0 48 108 35 70 90 84 68 68 283 276 .497 2.011 1.936 2.154 2.275 2.784 32 171 3.393 .46 60 4130 6820 35 41 270 276 0 240 73 167 1.781 235 161 .561 1.715 .833 .778
18 103 85 84 76 18 9 94 76 92 98 10 0 0 0 40 50 34 86 28 5 13 0 27 10 2 .5 null 2.202 1.633 5.18 52 345 7.825 .27 90 4280 6810 32 41 283 292 -50 75 67 8 .443 67 0 2.258 null -1.175 null
19 566 490 85 80 480 410 554 506 90 94 469 426 0 0 99 111 29 57 100 96 100 96 890 895 1.171 .854 .908 .816 .885 1.883 32 230 .89 .86 70 4440 6810 33 40 300 307 0 434 71 363 .757 448 377 1.322 .805 -.402 -.314
20 1537 5657 86 75 1450 5582 1728 6286 95 92 1641 6211 0 0 590 1769 39 67 100 100 100 100 7032 7852 .26 3.85 3.785 4.071 3.81 1.921 32 171 3.944 .91 60 4580 6820 35 41 315 321 0 5011 66 4944 3.41 5568 5501 .293 3.353 1.77 1.745

Total number of rows: 44544

Table truncated, full table size 9646 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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