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Sample GSM989715 Query DataSets for GSM989715
Status Public on Aug 23, 2012
Title PC 21T3
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 21T2.1
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 62
pre-operation treatment: None
individual: PC 26T
disease free survival: 60.30
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/2008-09/81253.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 GPL15971
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 13715 10235 38 98 13677 10136 13916 10239 40 107 13877 10140 0 0 1456 1339 7 54 100 100 100 100 23813 24017 1.349 .741 .731 .739 .74 2.575 52 364 .724 .98 90 1800 7380 29 38 31 40 0 10836 104 10731 .785 10840 10735 1.275 .774 -.35 -.37
2 14415 10104 41 97 14374 10007 14463 10105 42 106 14422 10008 0 0 1366 1606 9 56 100 100 100 100 24381 24430 1.436 .696 .694 .689 .696 2.643 52 294 .69 .98 90 1950 7380 29 38 46 55 0 10697 103 10595 .737 10698 10596 1.357 .735 -.44 -.445
3 13084 19010 42 94 13042 18916 15301 22099 43 104 15259 22005 0 0 5345 8482 10 56 100 98 100 97 31958 37264 .689 1.45 1.442 1.317 1.462 3.55 80 335 1.468 .98 100 2120 7370 28 38 63 73 0 20126 100 20027 1.536 23397 23297 .651 1.527 .619 .61
4 13157 8392 40 98 13117 8293 14073 8900 42 107 14032 8801 0 0 3355 2661 11 59 100 98 100 98 21410 22833 1.582 .632 .627 .589 .635 3.414 80 362 .636 .98 110 2260 7380 28 39 76 87 0 8885 104 8780 .669 9423 9318 1.494 .664 -.579 -.591
5 709 285 41 97 668 188 757 284 47 103 716 186 0 0 225 107 20 51 98 93 98 77 856 902 3.553 .281 .26 .26 .279 5.093 80 319 .276 .81 100 2410 7370 28 38 92 102 0 302 103 199 .298 301 197 3.356 .275 -1.747 -1.862
6 6824 9164 50 104 6773 9060 6690 9294 59 115 6639 9189 0 0 1086 1565 29 62 100 100 100 100 15833 15828 .748 1.338 1.384 1.33 1.345 2.671 80 330 1.322 .99 110 2550 7380 28 39 105 116 0 9702 110 9592 1.416 9840 9729 .706 1.465 .502 .551
7 198 235 46 103 152 132 201 229 51 115 155 126 0 0 39 86 22 60 100 76 100 50 284 281 1.152 .868 .813 .713 .891 5.672 52 272 .87 .54 90 2720 7380 29 38 123 132 0 249 109 140 .919 242 133 1.088 .861 -.121 -.217
8 13569 19827 41 101 13527 19725 15074 21695 44 112 15033 21593 0 0 4487 7083 15 53 100 100 100 100 33252 36626 .686 1.458 1.436 1.48 1.452 3.354 80 357 1.461 .99 110 2860 7370 27 38 136 147 0 20991 107 20883 1.544 22969 22861 .648 1.521 .627 .605
9 150 115 39 98 111 16 159 101 43 107 119 3 0 0 44 71 16 54 92 22 90 12 127 122 6.938 .144 .025 .32 .406 8.335 80 333 .119 .09 100 3010 7380 29 39 152 162 0 122 104 17 .153 107 3 6.553 .027 -2.712 -5.228
10 138 109 39 104 98 4 138 97 41 112 98 -7 0 0 36 50 9 53 96 18 95 3 102 91 24.5 .041 null .499 .442 7.803 80 364 -1 -1 100 3160 7380 29 39 167 177 0 115 110 4 .043 103 -7 23.141 null -4.532 null
11 773 1430 42 98 730 1331 782 1419 44 112 740 1321 0 0 204 419 11 66 97 98 97 98 2061 2061 .548 1.823 1.785 1.932 1.766 3.812 80 320 1.823 .94 110 3310 7380 28 39 181 192 0 1514 104 1409 1.93 1502 1399 .518 1.89 .949 .918
12 513 643 43 114 470 529 497 620 46 124 454 506 0 0 91 209 16 66 100 100 100 100 999 960 .888 1.126 1.115 1.061 1.046 3.421 80 304 1.184 .88 110 3460 7380 28 39 196 207 0 681 121 560 1.192 656 536 .839 1.18 .253 .239
13 378 332 41 114 337 218 382 329 44 126 341 215 0 0 98 138 11 68 100 80 100 67 555 556 1.546 .647 .63 .543 .633 5.321 80 318 .62 .72 100 3610 7370 28 38 212 222 0 351 121 231 .685 348 228 1.46 .668 -.546 -.583
14 146 224 40 104 105 120 144 220 42 117 103 115 0 0 21 92 9 72 100 70 100 33 225 218 .875 1.143 1.117 .862 1.087 7.061 80 358 1.513 .54 110 3760 7380 28 39 226 237 0 237 110 127 1.21 233 122 .826 1.182 .275 .241
15 46 147 42 74 3 72 46 152 43 86 3 77 0 0 6 48 9 48 16 83 0 25 75 80 .042 24 25.667 12.634 14.25 4.877 12 40 3.992 .34 40 3840 7380 32 36 238 242 0 156 78 76 25.409 161 82 .039 27.174 4.667 4.764
16 1417 2608 40 106 1376 2502 1607 2816 42 117 1566 2710 0 0 436 902 9 60 100 97 100 97 3878 4276 .55 1.818 1.731 1.732 1.746 3.36 80 362 1.847 .96 110 4070 7380 28 39 257 268 0 2761 112 2649 1.925 2981 2869 .519 1.832 .945 .874
17 114 107 38 107 75 0 112 97 39 118 73 -10 0 0 31 47 6 65 97 12 96 0 75 63 null null null .497 .645 7.295 80 229 .166 .08 100 4210 7370 28 38 272 282 0 113 113 0 null 103 -11 null null null null
18 42 92 40 118 2 -25 42 85 42 133 1 -33 0 0 6 45 9 77 15 4 0 0 -23 -32 null null null 9.898 9.474 9.69 120 337 130.743 .04 120 4360 7370 27 39 286 298 -100 97 125 -26 null 90 -35 null null null null
19 650 633 42 114 608 519 647 601 44 124 605 487 0 0 143 199 10 63 100 100 100 98 1127 1092 1.171 .854 .805 .818 .862 3.499 80 304 .838 .89 110 4510 7370 27 38 301 312 0 670 121 549 .904 636 516 1.107 .852 -.146 -.231
20 2801 10084 41 115 2760 9969 2917 10200 43 130 2876 10084 0 0 755 2477 9 76 100 100 100 100 12729 12960 .277 3.612 3.506 3.836 3.583 3.39 80 320 3.64 .98 100 4670 7370 28 38 318 328 0 10676 122 10554 3.824 10799 10676 .262 3.712 1.935 1.892

Total number of rows: 44544

Table truncated, full table size 9565 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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