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Sample GSM989759 Query DataSets for GSM989759
Status Public on Aug 23, 2012
Title PC 563T
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 563T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 71
pre-operation treatment: None
individual: PC 619T
disease free survival: 3.30
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/2008-08/81160.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 1484 1149 107 63 1377 1085 1330 1024 110 66 1223 960 0 0 627 501 32 25 100 100 100 100 2462 2183 1.269 .788 .785 .78 .783 1.187 52 372 .744 .93 90 1890 7000 19 28 36 45 0 1123 62 1060 .77 1001 938 1.298 .767 -.377 -.382
2 1065 729 116 53 948 675 1038 703 119 57 922 649 0 0 259 241 40 26 100 100 100 100 1623 1571 1.404 .712 .704 .67 .697 1.422 52 304 .711 .89 90 2050 7000 19 28 52 61 0 713 52 660 .696 687 634 1.437 .688 -.523 -.54
3 1363 2540 117 68 1245 2472 1318 2617 119 72 1200 2549 0 0 392 729 41 32 100 100 100 100 3717 3749 .504 1.986 2.124 1.975 1.94 1.175 52 279 2.004 .9 90 2190 7010 20 29 66 75 0 2483 66 2416 1.941 2558 2491 .515 2.076 .957 1.054
4 882 592 117 74 764 518 860 618 123 80 742 543 0 0 289 287 40 37 100 93 98 93 1282 1285 1.475 .678 .732 .596 .713 1.875 80 338 .714 .86 100 2350 7000 19 29 82 92 0 579 72 506 .663 604 531 1.509 .715 -.594 -.483
5 257 61 122 68 134 -6 246 56 134 81 124 -12 0 0 80 32 59 64 84 7 51 0 128 112 null null null .199 .232 3.332 52 227 -.089 -.16 80 2480 6990 19 27 96 104 0 60 66 -6 null 55 -12 null null null null
6 943 875 115 75 827 800 951 833 126 82 835 758 0 0 214 240 51 35 100 100 100 100 1627 1593 1.034 .967 .908 .951 .965 1.205 52 306 .926 .89 90 2640 6990 18 27 111 120 0 855 73 782 .945 814 741 1.058 .887 -.081 -.173
7 184 71 123 78 61 -6 176 66 125 82 53 -12 0 0 58 29 43 36 57 9 28 0 55 41 null null null .648 .832 3.324 52 296 -.329 -.13 90 2790 6990 18 27 126 135 -50 69 76 -6 null 65 -12 null null null null
8 1086 1739 119 72 966 1666 1000 1748 125 75 880 1675 0 0 258 407 39 29 100 100 100 100 2632 2555 .58 1.725 1.903 1.714 1.834 1.28 52 290 1.781 .89 90 2950 6990 18 27 142 151 0 1700 70 1628 1.686 1708 1637 .593 1.86 .753 .896
9 177 73 119 78 57 -4 168 73 126 97 48 -4 0 0 43 23 41 120 59 0 23 0 53 44 null null null .266 .286 3.28 52 279 -1 -1 90 3090 6990 18 27 156 165 -50 71 76 -4 null 71 -4 null null null null
10 177 82 116 72 61 9 177 80 123 86 61 7 0 0 42 27 41 108 65 0 21 0 70 68 6.778 .148 .115 .3 .268 3.616 52 312 .272 .13 90 3240 6990 18 27 171 180 -50 80 70 9 .144 78 7 6.935 .112 -2.794 -3.156
11 207 147 118 72 88 74 212 142 123 79 93 70 0 0 61 52 39 36 68 71 53 46 162 163 1.189 .841 .753 .934 .916 2.823 32 170 .644 .34 60 3400 6980 19 25 189 195 0 144 70 72 .822 139 68 1.217 .736 -.283 -.443
12 205 122 113 68 92 54 201 113 117 72 87 45 0 0 54 46 35 30 87 61 65 37 146 132 1.704 .587 .517 .528 .592 2.451 80 364 .543 .4 100 3550 6980 17 27 202 212 0 119 66 53 .574 110 44 1.743 .506 -.802 -.984
13 194 67 113 63 81 3 186 65 119 65 72 1 0 0 54 30 39 28 73 25 44 1 84 73 27 .037 .014 .189 .19 3.299 52 285 .1 .11 90 3690 6980 17 26 216 225 -50 65 62 3 .036 64 1 27.624 .014 -4.788 -6.203
14 201 82 119 67 81 14 199 74 123 72 79 7 0 0 49 29 37 31 80 25 53 11 95 86 5.786 .173 .089 .279 .294 3.634 52 309 .08 .1 90 3840 6980 17 26 231 240 -50 80 65 14 .169 72 7 5.92 .087 -2.565 -3.529
15 173 56 116 73 56 -16 173 53 121 77 56 -20 0 0 50 21 36 31 61 3 36 0 40 36 null null null .289 .378 4.006 52 300 -.161 -.09 90 3990 6980 17 26 246 255 -50 55 71 -16 null 52 -20 null null null null
16 305 141 121 70 184 70 314 141 133 74 193 70 0 0 129 67 69 30 76 71 65 53 254 263 2.629 .38 .363 .409 .43 2.739 52 316 .293 .6 90 4140 6980 17 26 261 270 -50 138 68 68 .372 138 68 2.689 .354 -1.427 -1.496
17 255 107 119 75 136 31 263 100 124 80 143 25 0 0 53 29 39 32 96 40 81 12 167 168 4.387 .228 .175 .223 .245 1.946 32 221 .203 .28 70 4300 6980 18 25 278 285 0 105 73 30 .223 98 24 4.489 .171 -2.166 -2.549
18 189 54 111 69 78 -14 188 52 116 74 77 -16 0 0 46 17 37 31 82 0 53 0 64 61 null null null .152 .179 1.914 52 303 -.238 -.18 90 4450 6980 17 26 292 301 -50 53 67 -14 null 51 -16 null null null null
19 234 143 110 65 124 78 221 149 115 71 111 84 0 0 64 53 34 31 96 80 84 61 202 195 1.59 .629 .757 .699 .715 1.958 52 291 .584 .46 90 4600 6980 17 26 307 316 0 140 64 76 .615 146 82 1.627 .74 -.702 -.435
20 293 428 115 74 177 353 279 427 119 81 163 352 0 0 71 117 38 36 100 100 96 100 530 515 .501 1.994 2.16 2.022 2.111 1.536 52 282 2.288 .7 90 4750 6990 18 27 322 331 0 418 72 345 1.949 417 344 .513 2.111 .963 1.078

Total number of rows: 44544

Table truncated, full table size 9656 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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