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Sample GSM989687 Query DataSets for GSM989687
Status Public on Aug 23, 2012
Title PC 626T
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 626T2.0
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 62
pre-operation treatment: None
individual: PC 351T
disease free survival: 62.30
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/2008-08/81157.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 8203 4635 70 65 8133 4569 9201 5307 73 77 9131 5241 0 0 2921 1693 23 56 100 100 100 100 12702 14372 1.78 .562 .574 .565 .57 1.724 52 305 .556 .98 80 1800 7300 26 34 32 40 0 4337 61 4275 .526 4965 4904 1.903 .537 -.928 -.897
2 7653 4842 72 75 7580 4766 8979 5407 77 84 8906 5331 0 0 3204 1911 24 59 100 100 100 96 12346 14237 1.59 .629 .599 .654 .611 1.684 52 254 .61 .97 80 1950 7300 26 34 47 55 0 4530 70 4459 .588 5059 4988 1.7 .56 -.765 -.836
3 16922 34729 74 63 16847 34665 18637 36938 82 75 18562 36875 0 0 5957 10381 33 69 100 100 100 100 51512 55437 .486 2.058 1.987 2.169 1.966 1.724 52 277 2.017 .98 90 2090 7320 27 36 60 69 0 32493 59 32433 1.925 34560 34501 .519 1.859 .945 .894
4 10650 6026 74 77 10575 5949 10501 5962 80 84 10427 5885 0 0 1442 778 25 40 100 100 100 100 16524 16312 1.778 .563 .564 .563 .572 1.311 52 300 .555 .98 90 2250 7320 27 36 76 85 0 5638 72 5566 .526 5578 5506 1.9 .528 -.926 -.921
5 931 221 84 73 847 147 899 219 88 82 814 145 0 0 102 69 28 42 100 93 100 87 994 959 5.762 .174 .178 .15 .162 2.273 32 221 .155 .75 70 2400 7300 26 33 92 99 0 207 68 138 .162 205 136 6.158 .167 -2.623 -2.585
6 8009 7125 100 75 7908 7049 8691 8155 111 86 8590 8079 0 0 3814 3184 42 55 100 100 100 98 14957 16669 1.122 .891 .941 .901 .883 1.862 80 321 .874 .97 100 2560 7310 26 36 107 117 0 6666 70 6595 .834 7630 7559 1.199 .88 -.262 -.184
7 241 110 87 81 153 28 238 111 96 89 150 29 0 0 56 37 34 38 100 28 90 9 181 179 5.464 .183 .193 .227 .258 2.85 52 238 .193 .24 80 2700 7300 26 34 122 130 0 103 76 26 .171 104 27 5.84 .181 -2.546 -2.467
8 18246 33150 84 77 18162 33073 19866 36002 87 85 19782 35925 0 0 5511 8954 27 51 100 100 100 100 51235 55707 .549 1.821 1.816 1.857 1.784 1.576 52 251 1.813 .98 80 2850 7300 26 34 137 145 0 31016 72 30944 1.704 33684 33612 .587 1.699 .769 .765
9 139 141 88 74 50 66 121 133 91 84 32 58 0 0 64 56 27 49 53 57 38 28 116 90 .758 1.32 1.813 1.761 1.699 4.281 52 292 1.172 .55 90 2990 7300 25 34 150 159 -50 132 69 62 1.235 124 54 .81 1.696 .305 .762
10 227 204 104 92 122 112 218 181 108 99 114 89 0 0 92 67 29 50 84 90 78 43 234 203 1.089 .918 .781 .958 .799 2.732 32 171 .817 .55 60 3140 7310 28 34 167 173 0 191 86 105 .859 169 83 1.164 .73 -.219 -.453
11 667 1078 113 72 554 1005 654 1098 117 83 541 1026 0 0 246 364 34 44 98 100 96 100 1559 1567 .551 1.814 1.896 1.892 1.839 1.611 52 265 1.79 .94 80 3310 7300 26 34 183 191 0 1009 67 940 1.697 1027 960 .589 1.774 .763 .827
12 468 2435 116 83 351 2351 455 2534 121 95 338 2451 0 0 215 1157 40 57 90 96 86 96 2702 2789 .149 6.698 7.251 6.897 7.31 2 80 322 7.052 .89 100 3460 7300 25 35 197 207 0 2278 78 2200 6.267 2371 2293 .16 6.785 2.648 2.762
13 440 341 123 87 316 253 414 331 128 98 291 243 0 0 118 99 32 49 98 100 98 90 569 534 1.249 .801 .835 .802 .859 1.932 52 225 .768 .8 80 3610 7300 26 34 213 221 0 319 81 237 .749 310 227 1.335 .781 -.417 -.356
14 182 200 87 80 94 119 176 205 112 131 88 125 0 0 47 68 245 619 0 0 0 0 213 213 .79 1.266 1.42 1.171 1.149 2.698 52 243 1.093 .55 80 3750 7300 26 34 227 235 0 187 75 111 1.184 192 117 .844 1.329 .244 .41
15 80 62 73 83 6 -21 76 59 95 121 2 -23 0 0 18 24 214 539 0 0 0 0 -15 -21 null null null 2.667 2.525 4.861 52 320 2.603 .96 90 3900 7290 24 33 241 250 -50 58 78 -20 null 55 -22 null null null null
16 2517 1127 75 78 2442 1049 2948 1230 82 89 2872 1152 0 0 1342 632 52 65 95 91 93 85 3491 4024 2.328 .43 .401 .38 .42 3.064 80 362 .425 .95 100 4060 7290 24 34 257 267 0 1054 73 981 .402 1151 1078 2.488 .375 -1.315 -1.414
17 95 131 73 69 21 62 94 134 78 80 20 65 0 0 23 46 30 60 36 53 5 5 83 85 .339 2.952 3.25 2.335 2.29 3.955 52 267 5.177 .29 90 4200 7290 24 33 271 280 -50 123 65 58 2.762 125 61 .362 3.041 1.466 1.604
18 78 62 75 84 2 -22 76 53 83 97 0 -31 0 0 16 28 36 78 3 0 0 0 -20 -31 null null null 3.535 3.015 4.887 52 318 2.593 .69 90 4350 7290 24 33 286 295 -50 58 79 -21 null 50 -29 null null null null
19 526 440 80 80 445 360 528 434 86 94 448 354 0 0 143 119 32 64 100 100 100 100 805 802 1.236 .809 .79 .804 .797 1.57 52 332 .791 .89 90 4510 7290 24 33 302 311 0 412 75 337 .757 406 331 1.321 .739 -.402 -.436
20 2714 6062 77 81 2637 5981 2784 6120 83 90 2706 6039 0 0 508 1331 26 46 100 100 100 100 8618 8745 .441 2.268 2.232 2.254 2.3 1.445 52 268 2.328 .97 80 4660 7290 25 33 318 326 0 5672 76 5596 2.122 5726 5650 .471 2.088 1.085 1.062

Total number of rows: 44544

Table truncated, full table size 9519 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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