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Sample GSM989741 Query DataSets for GSM989741
Status Public on Aug 23, 2012
Title PC 593T
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 593T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 54
pre-operation treatment: None
individual: PC 626T
disease free survival: 1.37
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/2008-08/81145.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 22790 13942 80 130 22710 13811 22738 13646 84 143 22658 13515 0 0 3630 2476 23 64 100 100 100 100 36521 36173 1.644 .608 .596 .607 .599 1.6 52 284 .614 .98 80 2080 6850 37 45 40 48 0 11720 109 11610 .511 11472 11361 1.956 .501 -.968 -.996
2 16566 10385 85 136 16480 10248 17614 10610 94 150 17528 10473 0 0 4086 2625 39 69 100 100 100 100 26728 28001 1.608 .622 .598 .622 .611 1.922 52 289 .611 .98 90 2220 6840 35 44 53 62 0 8730 114 8615 .523 8919 8804 1.913 .502 -.936 -.993
3 17771 24478 98 152 17672 24326 22065 28471 149 202 21966 28318 0 0 8916 11253 390 346 92 92 90 92 41998 50284 .726 1.377 1.289 1.471 1.334 2.067 52 301 1.343 .99 90 2370 6840 35 44 68 77 0 20578 128 20450 1.157 23934 23806 .864 1.084 .211 .116
4 18227 11105 97 147 18130 10957 18095 10773 145 204 17997 10625 0 0 2199 1698 395 361 100 100 100 100 29087 28622 1.655 .604 .59 .602 .596 1.637 52 291 .606 .98 90 2530 6840 35 44 84 93 0 9336 124 9211 .508 9056 8932 1.968 .496 -.977 -1.011
5 1019 301 102 140 917 161 1003 292 128 167 901 151 0 0 206 73 94 129 100 59 100 9 1078 1052 5.696 .176 .168 .159 .164 2.512 52 253 .177 .76 80 2680 6830 35 43 100 108 0 253 118 135 .148 245 127 6.775 .141 -2.76 -2.827
6 10305 7591 204 167 10100 7424 9714 7208 225 185 9509 7041 0 0 2567 1754 115 105 100 100 100 100 17524 16550 1.36 .735 .74 .739 .719 1.687 52 282 .728 .99 90 2830 6830 34 43 114 123 0 6381 140 6241 .618 6059 5919 1.618 .622 -.694 -.684
7 268 129 103 156 164 -26 268 123 127 180 164 -32 0 0 72 44 75 117 88 0 65 0 138 132 null null null .148 .14 8.129 52 278 -1 -1 90 2970 6830 34 43 128 137 -50 108 131 -22 null 103 -27 null null null null
8 11871 16240 81 158 11790 16082 17460 23305 336 500 17379 23146 0 0 8825 12274 1779 2359 73 69 63 65 27872 40525 .733 1.364 1.332 1.251 1.344 2.87 52 296 1.387 .99 90 3120 6830 34 43 143 152 -100 13652 133 13519 1.147 19592 19458 .872 1.12 .197 .163
9 118 107 77 144 41 -36 118 89 255 368 41 -54 0 0 34 88 1401 1830 0 0 0 0 5 -13 null null null 2.364 3.371 11.472 52 306 8.245 .24 90 3280 6830 34 43 159 168 -50 90 121 -30 null 75 -45 null null null null
10 118 145 74 151 44 -6 117 136 80 172 43 -14 0 0 23 59 33 111 63 3 21 0 38 29 null null null .971 1.259 5.528 52 292 9.926 .2 90 3430 6830 34 43 174 183 -50 122 127 -5 null 114 -12 null null null null
11 408 728 76 147 331 580 391 717 77 157 315 569 0 0 85 179 20 71 100 100 100 100 911 884 .571 1.752 1.806 1.73 1.786 2.011 52 262 1.813 .92 80 3580 6830 35 43 190 198 0 612 124 488 1.473 603 478 .679 1.519 .559 .603
12 332 996 73 149 258 847 324 948 80 161 251 798 0 0 94 235 27 75 100 100 98 100 1105 1049 .305 3.283 3.179 3.415 3.415 2.193 52 282 3.395 .92 90 3730 6830 34 43 204 213 0 837 125 712 2.76 797 671 .362 2.673 1.465 1.418
13 250 198 68 136 182 61 248 191 73 149 179 54 0 0 48 67 22 84 100 36 100 5 243 233 2.984 .335 .302 .28 .37 4.533 52 253 .485 .43 80 3880 6820 34 42 220 228 0 166 114 51 .282 161 45 3.549 .254 -1.827 -1.979
14 138 160 71 145 66 14 145 160 77 160 74 14 0 0 41 60 24 88 84 13 69 0 80 88 4.714 .212 .189 .965 .793 2.946 52 272 4.045 .25 90 4030 6830 34 43 234 243 -50 135 122 12 .178 135 12 5.608 .159 -2.487 -2.653
15 65 56 80 152 -14 -95 63 49 85 168 -16 -103 0 0 12 30 36 94 0 0 0 0 -109 -119 null null null 5.005 5.293 3.854 52 272 3.568 .63 90 4180 6830 34 43 249 258 -50 47 128 -80 null 41 -87 null null null null
16 1671 1465 80 158 1591 1306 1690 1482 84 169 1610 1323 0 0 320 288 28 82 100 100 100 100 2897 2933 1.218 .821 .822 .819 .804 1.8 52 253 .806 .97 90 4330 6840 35 44 264 273 0 1232 133 1098 .69 1246 1112 1.449 .691 -.535 -.534
17 85 129 75 143 9 -13 84 127 81 156 9 -15 0 0 20 52 27 67 17 5 1 1 -4 -6 null null null 2.111 2.286 5.481 52 272 7.186 .25 90 4480 6830 34 43 279 288 -50 108 120 -11 null 107 -13 null null null null
18 701 2107 80 150 621 1956 57 58 84 169 -22 -92 0 0 3467 8735 32 84 13 13 11 13 2577 -114 .317 3.15 null 4.154 3.493 3.472 52 291 2.764 .93 90 4630 6820 33 42 294 303 -50 1771 126 1644 2.648 49 -77 .378 null 1.405 null
19 330 254 83 161 247 93 302 246 86 180 219 84 0 0 122 95 23 84 96 50 96 21 340 303 2.656 .377 .384 .384 .408 3.738 52 259 .457 .49 80 4780 6820 34 42 310 318 0 214 135 78 .317 207 71 3.159 .322 -1.66 -1.633
20 1454 3570 84 161 1369 3409 1531 3697 88 179 1446 3536 0 0 404 940 25 93 100 100 100 100 4778 4982 .402 2.49 2.445 2.558 2.403 1.923 52 255 2.489 .98 90 4930 6840 35 44 324 333 0 3001 135 2866 2.093 3108 2973 .478 2.056 1.066 1.04

Total number of rows: 44544

Table truncated, full table size 9457 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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