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Sample GSM989745 Query DataSets for GSM989745
Status Public on Aug 23, 2012
Title PC 265T
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 265T2
Organism Homo sapiens
Characteristics ethnicity: African American
age: 57
pre-operation treatment: Hormonal
individual: PC 366T
disease free survival: 12.33
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/2008-08/81080.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 19466 13517 95 57 19371 13459 24425 18041 101 65 24330 17984 0 0 10201 7410 33 40 100 100 100 100 32830 42314 1.439 .695 .739 .616 .655 2.02 32 232 .712 .9 70 2010 7110 59 66 89 96 0 11413 48 11364 .587 15232 15184 1.705 .624 -.769 -.68
2 15374 10591 93 56 15281 10534 17274 11024 98 67 17180 10967 0 0 11419 8191 28 43 100 100 93 96 25815 28147 1.451 .689 .638 .881 .699 4.168 32 176 .711 .88 60 2150 7120 61 67 104 110 0 8942 47 8894 .582 9308 9260 1.718 .539 -.781 -.892
3 3979 8331 88 61 3890 8270 1016 1820 101 79 927 1759 0 0 4702 10191 67 79 82 90 73 71 12160 2686 .47 2.126 1.898 1.821 2.24 2.732 52 348 2.407 .88 90 2310 7110 58 67 118 127 0 7034 52 6983 1.795 1537 1485 .557 1.602 .844 .68
4 20151 13080 95 68 20055 13011 25546 17839 105 111 25451 17770 0 0 10671 7940 50 231 100 100 100 96 33066 43221 1.541 .649 .698 .563 .665 1.745 32 165 .684 .9 60 2460 7120 61 67 135 141 0 11044 57 10985 .548 15062 15004 1.826 .59 -.868 -.762
5 534 400 101 75 432 324 534 425 108 89 432 349 0 0 300 217 46 67 90 81 87 75 756 781 1.333 .75 .808 .79 .767 1.852 32 169 .78 .84 60 2610 7110 60 66 150 156 0 338 63 274 .633 359 295 1.579 .682 -.659 -.552
6 7384 10934 116 81 7268 10853 9026 14877 126 105 8910 14796 0 0 4339 6576 56 89 100 100 100 100 18121 23706 .67 1.493 1.661 1.589 1.501 1.779 52 333 1.561 .95 90 2760 7110 58 67 163 172 0 9232 68 9163 1.261 12561 12493 .793 1.402 .334 .488
7 265 219 103 79 161 139 257 191 116 109 153 111 0 0 85 127 55 111 93 50 71 25 300 264 1.158 .863 .725 .703 .576 2.553 32 189 7.964 .22 70 2920 7120 60 67 180 187 0 185 67 117 .729 161 94 1.372 .613 -.456 -.707
8 5436 12573 98 68 5337 12505 2713 7864 111 91 2615 7796 0 0 5266 11591 61 98 86 90 84 76 17842 10411 .427 2.343 2.981 2.132 2.245 2.217 52 228 2.378 .94 80 3050 7110 59 67 193 201 0 10616 57 10558 1.978 6640 6582 .505 2.517 .984 1.332
9 168 81 93 68 75 12 117 65 103 99 23 -3 0 0 205 67 42 147 36 3 17 1 87 20 6.25 .16 null .458 .334 4.41 52 302 11.016 .23 90 3190 7110 58 67 206 215 -50 68 57 10 .135 55 -3 7.402 null -2.888 null
10 155 336 100 63 55 273 138 187 111 91 38 123 0 0 88 539 50 113 25 58 25 16 328 161 .201 4.964 3.237 2.582 2.678 7.422 12 68 -196.86 -.03 40 3340 7110 61 65 224 228 0 284 53 230 4.191 158 104 .239 2.733 2.067 1.45
11 352 746 98 71 253 674 395 814 108 95 296 742 0 0 158 281 45 85 84 96 75 90 927 1038 .375 2.664 2.507 3.018 2.35 1.633 32 233 2.799 .79 70 3510 7110 59 66 239 246 0 630 60 569 2.249 687 626 .445 2.117 1.169 1.082
12 405 742 98 68 306 673 427 770 108 97 328 701 0 0 148 287 51 100 96 96 87 90 979 1029 .455 2.199 2.137 2.18 2.277 1.313 32 236 2.507 .84 70 3660 7120 60 67 254 261 0 626 57 568 1.857 650 592 .539 1.804 .893 .852
13 256 183 92 62 163 121 248 183 101 83 156 120 0 0 97 57 41 68 93 87 84 37 284 276 1.347 .742 .769 .808 .743 1.27 32 169 1.67 .81 60 3820 7110 60 66 271 277 0 155 52 102 .627 155 101 1.595 .649 -.674 -.623
14 147 115 96 66 51 49 130 101 108 92 33 35 0 0 72 82 56 93 38 17 15 3 100 68 1.041 .961 1.061 .697 .826 2.121 52 295 3.326 .41 90 3960 7110 58 67 283 292 -50 97 56 41 .811 85 30 1.233 .895 -.302 -.159
15 105 49 95 69 10 -19 98 41 107 93 3 -27 0 0 42 29 47 114 11 0 5 0 -9 -24 null null null 1.214 1.353 3.6 52 312 8.799 .16 90 4110 7110 58 67 298 307 -50 41 58 -16 null 35 -23 null null null null
16 1244 1116 101 72 1143 1043 1296 1189 115 106 1195 1117 0 0 361 403 58 147 100 96 100 93 2186 2312 1.096 .913 .935 .867 .873 1.132 32 224 .978 .9 70 4270 7100 58 65 315 322 0 942 61 881 .77 1004 943 1.298 .789 -.376 -.342
17 160 120 98 71 61 48 125 104 112 100 26 32 0 0 120 97 71 97 28 17 7 3 109 58 1.271 .787 1.231 1.022 1.191 2.29 52 323 2.716 .33 90 4410 7110 58 67 328 337 -50 101 60 41 .664 88 27 1.505 1.039 -.59 .055
18 92 70 92 71 0 0 88 55 102 94 -3 -15 0 0 28 56 43 94 7 3 1 1 0 -18 null null null 1.5 1.407 2.302 52 313 10.493 .2 90 4570 7110 58 67 344 353 -50 59 60 0 null 46 -13 null null null null
19 539 1226 95 71 443 1155 405 399 108 101 310 328 0 0 680 3337 61 109 90 96 84 78 1598 638 .384 2.607 1.058 1.339 1.168 2.298 32 224 36.421 .12 70 4720 7110 59 66 360 367 0 1035 60 975 2.201 337 277 .454 .893 1.138 -.163
20 1779 4059 97 68 1682 3990 1980 5045 110 92 1883 4976 0 0 875 2439 52 75 100 100 96 100 5672 6859 .422 2.372 2.643 2.022 2.229 1.57 32 212 2.675 .92 70 4880 7110 59 66 376 383 0 3427 57 3369 2.003 4260 4201 .499 2.231 1.002 1.158

Total number of rows: 44544

Table truncated, full table size 9408 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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