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Sample GSM989789 Query DataSets for GSM989789
Status Public on Aug 23, 2012
Title PC 86T
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 86T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 61
pre-operation treatment: None
individual: PC 643T
disease free survival: 18.07
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/2008-08/81118.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 3183 1903 79 115 3104 1788 3932 2178 83 132 3852 2063 0 0 1368 1135 25 79 100 90 100 86 4892 5915 1.736 .576 .536 .53 .63 3.505 52 316 .571 .85 80 1790 6830 23 31 47 55 0 1522 92 1430 .461 1742 1650 2.17 .428 -1.118 -1.223
2 3939 1685 90 139 3849 1545 4063 1914 93 151 3973 1775 0 0 847 808 24 78 100 93 100 90 5394 5748 2.491 .401 .447 .308 .434 3.249 32 216 .417 .85 70 1940 6820 22 29 62 69 0 1348 111 1236 .321 1531 1420 3.114 .357 -1.639 -1.484
3 3562 4854 89 133 3472 4721 4811 5614 94 166 4722 5480 0 0 2397 4269 33 149 88 71 82 65 8193 10202 .735 1.36 1.161 .915 1.541 5.945 52 333 1.71 .89 90 2090 6820 21 30 76 85 0 3883 106 3777 1.088 4491 4384 .919 .928 .121 -.107
4 3471 1335 83 136 3388 1198 3599 1493 89 158 3516 1356 0 0 649 579 34 149 100 90 100 84 4586 4872 2.828 .354 .386 .314 .385 2.45 52 240 .371 .86 80 2250 6820 22 30 93 101 0 1068 109 958 .283 1194 1085 3.535 .309 -1.822 -1.697
5 202 169 86 122 115 47 206 153 91 135 120 31 0 0 77 107 25 67 78 40 71 25 162 151 2.447 .409 .258 1.732 2.357 5.584 32 155 -.643 -.19 60 2370 6810 22 28 106 112 0 135 98 38 .327 122 25 3.059 .207 -1.613 -2.275
6 2068 1718 110 126 1958 1592 2385 1992 128 140 2275 1866 0 0 1078 867 119 74 88 88 84 88 3550 4141 1.23 .813 .82 .839 .847 2.175 52 251 .729 .83 90 2530 6850 24 33 120 129 0 1374 101 1274 .65 1594 1493 1.537 .656 -.621 -.608
7 105 129 94 134 10 -5 105 99 111 150 10 -35 0 0 24 84 110 82 0 15 0 3 5 -25 null null null 3.092 4.89 5.177 52 306 -23.969 -.07 90 2680 6810 20 29 135 144 -50 103 107 -4 null 79 -28 null null null null
8 4594 7583 88 142 4505 7440 5512 9423 95 155 5423 9280 0 0 2134 3758 31 86 100 100 98 98 11945 14703 .606 1.651 1.711 1.632 1.725 5.129 52 245 1.739 .88 80 2840 6820 22 30 152 160 0 6066 114 5952 1.321 7538 7424 .757 1.369 .402 .453
9 68 112 88 136 -20 -24 64 109 94 153 -23 -27 0 0 15 54 30 88 0 1 0 0 -44 -50 null null null 1.938 2.043 4.473 52 291 14.494 .15 90 2990 6810 20 29 166 175 -50 90 109 -19 null 87 -22 null null null null
10 70 97 87 136 -16 -39 65 88 92 166 -22 -48 0 0 20 53 31 119 0 1 0 0 -55 -70 null null null 2.309 2.561 3.75 52 304 21.876 .17 90 3140 6810 20 29 181 190 -50 78 109 -31 null 70 -38 null null null null
11 154 225 83 123 70 101 156 234 88 152 72 110 0 0 48 78 30 121 78 43 59 3 171 182 .693 1.443 1.528 1.326 1.469 4.077 32 174 7.788 .17 60 3290 6820 23 29 198 204 0 180 98 81 1.154 187 88 .866 1.222 .207 .289
12 115 165 85 122 30 43 113 153 88 135 27 31 0 0 30 82 27 76 48 30 25 13 73 58 .698 1.433 1.148 2.35 2.199 4.414 52 320 -1 -1 90 3440 6810 20 29 211 220 -50 132 98 34 1.147 122 25 .872 .918 .197 -.123
13 96 109 88 139 7 -29 95 90 90 159 7 -48 0 0 21 63 24 104 13 5 3 0 -22 -41 null null null 3.166 2.988 7.56 52 309 43.264 .07 90 3590 6800 19 28 226 235 -50 87 111 -23 null 72 -38 null null null null
14 97 118 84 123 12 -4 95 92 89 148 10 -30 0 0 21 80 28 108 25 9 0 1 8 -20 null null null 3.805 3.869 6.588 52 309 -71.469 -.05 90 3740 6800 19 28 241 250 -50 94 98 -3 null 74 -24 null null null null
15 60 99 83 122 -22 -22 60 89 89 141 -22 -32 0 0 10 64 45 112 0 7 0 0 -44 -54 null null null 1.909 2.113 4.657 52 310 20.651 .09 90 3890 6800 19 28 256 265 -50 79 98 -18 null 71 -26 null null null null
16 659 341 87 138 571 203 658 339 97 165 570 201 0 0 132 151 51 138 100 67 100 25 774 771 2.813 .356 .353 .345 .412 2.661 52 251 .373 .61 80 4050 6800 20 28 273 281 0 273 110 162 .284 271 161 3.516 .282 -1.814 -1.826
17 70 104 87 126 -16 -22 64 87 95 174 -22 -39 0 0 20 70 48 258 0 1 0 0 -38 -61 null null null 2.012 2.59 3.75 52 279 12.726 .2 90 4190 6800 19 28 286 295 -50 83 101 -18 null 70 -31 null null null null
18 63 96 85 139 -22 -43 61 75 93 173 -23 -63 0 0 15 59 48 156 0 0 0 0 -65 -86 null null null 3.017 2.649 3.876 52 291 10.719 .21 90 4340 6800 19 28 301 310 -50 77 111 -34 null 60 -50 null null null null
19 129 142 83 135 45 6 127 125 93 168 43 -10 0 0 36 82 47 130 40 7 11 1 51 33 7.5 .133 null .897 1.505 8.963 52 306 -1 -1 90 4490 6800 19 28 316 325 -50 114 108 5 .107 100 -8 9.375 null -3.229 null
20 520 1030 83 127 437 903 575 1141 89 150 492 1013 0 0 205 457 28 98 94 92 92 88 1340 1505 .484 2.066 2.059 2.254 2.17 4.731 52 261 2.403 .78 80 4650 6800 20 28 333 341 0 824 102 722 1.653 913 810 .605 1.647 .725 .72

Total number of rows: 44544

Table truncated, full table size 9564 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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