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Sample GSM989749 Query DataSets for GSM989749
Status Public on Aug 23, 2012
Title PC 167T
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 167T2
Organism Homo sapiens
Characteristics ethnicity: African American
age: 59
pre-operation treatment: None
individual: PC 265T
disease free survival: 2.77
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/2008-08/81246.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 34708 30500 101 80 34607 30420 42804 37223 129 114 42703 37143 0 0 15953 13862 97 125 98 100 98 100 65027 79846 1.138 .879 .87 .95 .895 2.494 80 433 .869 .95 100 1780 6650 24 34 9 19 0 27401 72 27329 .79 33441 33369 1.266 .781 -.341 -.356
2 48228 45275 114 83 48113 45192 52258 49937 145 126 52144 49854 0 0 13170 12151 110 140 100 100 100 100 93305 101998 1.065 .939 .956 .946 .941 1.502 52 284 .923 .97 90 1930 6640 23 32 24 33 0 40674 75 40600 .844 44863 44788 1.185 .859 -.245 -.219
3 38290 44664 99 70 38190 44593 46693 53553 124 87 46594 53483 0 0 18375 21562 95 65 100 98 100 98 82783 100077 .856 1.168 1.148 1.027 1.166 3.491 80 346 1.165 .96 100 2080 6640 23 33 39 49 0 40126 63 40062 1.049 48111 48048 .953 1.031 .069 .044
4 47897 46758 108 82 47789 46676 50811 48885 137 97 50703 48803 0 0 10620 9654 102 69 100 98 100 98 94465 99506 1.024 .977 .963 .937 .969 1.758 80 334 .953 .94 110 2230 6660 24 35 53 64 0 42007 74 41933 .877 43918 43844 1.14 .865 -.189 -.21
5 2702 817 96 64 2606 753 2759 856 116 85 2663 792 0 0 747 247 84 69 100 100 98 98 3359 3455 3.461 .289 .297 .29 .283 1.647 80 318 .273 .9 110 2380 6650 23 34 68 79 0 734 57 676 .26 769 712 3.852 .267 -1.946 -1.904
6 21724 41673 102 77 21621 41596 21859 43674 203 177 21756 43596 0 0 5912 12294 527 385 98 100 98 100 63217 65352 .52 1.924 2.004 1.921 1.988 1.753 80 323 2.027 .94 110 2520 6650 23 34 82 93 0 37438 69 37369 1.728 39236 39166 .579 1.8 .789 .848
7 624 434 113 84 510 350 615 427 213 213 501 343 0 0 170 135 552 589 37 2 0 0 860 844 1.457 .686 .685 .671 .676 2.109 80 297 1.552 .4 100 2680 6660 25 35 99 109 0 390 75 314 .617 384 308 1.622 .615 -.698 -.701
8 40970 48226 90 63 40879 48163 48160 56495 113 114 48070 56432 0 5 17886 19232 98 397 100 97 97 97 89042 104502 .849 1.178 1.174 1.277 1.176 2.289 80 381 1.154 .97 110 2840 6640 22 33 114 125 0 43326 57 43269 1.058 50754 50698 .945 1.055 .082 .077
9 429 368 79 59 349 309 415 379 96 73 335 320 0 0 134 133 59 54 96 97 95 93 658 655 1.129 .885 .955 .841 .883 1.884 80 280 .884 .85 110 2990 6660 24 35 129 140 0 331 53 278 .795 340 287 1.257 .858 -.33 -.221
10 388 569 74 55 313 514 389 543 78 59 314 487 0 0 118 185 27 31 98 98 96 97 827 801 .609 1.642 1.551 1.654 1.609 1.692 80 312 1.739 .84 110 3130 6650 23 34 143 154 0 511 49 462 1.475 488 438 .678 1.393 .561 .479
11 1477 2848 78 53 1399 2795 1479 2796 82 64 1401 2743 0 0 444 788 30 56 100 100 98 98 4194 4144 .501 1.998 1.958 2.029 1.972 1.73 80 335 2.077 .92 110 3280 6650 23 34 158 169 0 2559 48 2511 1.795 2512 2464 .557 1.759 .844 .815
12 1090 6362 75 54 1014 6308 1093 6520 80 64 1017 6466 0 0 273 1656 30 56 100 100 100 100 7322 7483 .161 6.221 6.358 6.128 6.406 1.424 80 306 6.862 .91 110 3440 6650 23 34 174 185 0 5716 49 5667 5.589 5857 5809 .179 5.712 2.483 2.514
13 814 618 71 53 742 565 849 618 77 59 777 565 0 0 241 202 27 32 100 100 98 98 1307 1342 1.313 .761 .727 .759 .736 1.768 80 256 .687 .86 110 3590 6660 24 35 189 200 0 555 48 508 .684 555 508 1.462 .653 -.548 -.614
14 339 602 74 57 264 545 331 602 79 63 256 545 0 0 87 140 31 33 100 100 100 100 809 801 .484 2.064 2.129 2.097 2.203 1.533 80 346 2.194 .82 110 3730 6640 22 33 203 214 0 541 51 490 1.855 541 490 .539 1.913 .891 .936
15 104 62 70 55 33 7 101 55 78 59 30 0 0 0 32 33 31 31 47 17 15 5 40 30 4.714 .212 null .8 .711 6.146 120 395 1.11 .08 120 3880 6640 22 34 218 230 -50 56 49 6 .191 49 0 5.248 null -2.392 null
16 1489 1648 71 54 1418 1594 1781 1925 77 60 1709 1871 0 0 896 1042 27 33 92 90 90 88 3012 3580 .89 1.124 1.095 1.056 1.152 3.814 120 346 1.153 .92 120 4040 6650 23 35 234 246 0 1481 49 1432 1.01 1729 1681 .99 .984 .014 -.024
17 229 494 74 55 154 438 223 504 78 60 148 448 0 0 60 144 28 33 96 100 96 100 592 596 .352 2.844 3.027 3.023 2.851 2.027 80 350 3.274 .76 110 4190 6650 23 34 249 260 0 444 49 393 2.555 453 402 .391 2.719 1.353 1.443
18 88 61 76 52 11 9 83 54 79 59 6 2 0 0 33 40 28 34 22 19 8 5 20 8 1.222 .818 .333 1.301 1.188 3.319 120 437 10.23 .03 120 4340 6650 23 35 264 276 -50 55 47 8 .735 49 2 1.36 .299 -.444 -1.74
19 1153 1178 79 60 1073 1118 1200 1217 85 74 1120 1157 0 0 556 658 36 55 97 95 93 92 2191 2277 .96 1.042 1.033 .965 1.073 2.785 120 346 1.091 .9 120 4490 6650 23 35 279 291 0 1058 54 1004 .936 1093 1039 1.068 .928 -.095 -.108
20 6551 17377 83 61 6467 17316 6466 18047 90 76 6382 17986 0 0 1382 4311 36 57 100 100 100 100 23783 24368 .373 2.678 2.818 2.596 2.663 1.39 80 291 2.789 .95 110 4650 6650 23 34 295 306 0 15611 55 15556 2.406 16213 16158 .416 2.532 1.266 1.34

Total number of rows: 44544

Table truncated, full table size 9675 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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