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Sample GSM989808 Query DataSets for GSM989808
Status Public on Aug 23, 2012
Title PC 636T
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 636T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 54
pre-operation treatment: None
individual: PC 393T
disease free survival: 33.60
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/2008-08/81153.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 11350 7217 93 132 11256 7085 14970 9000 100 142 14876 8868 0 0 6646 3615 37 66 100 100 96 100 18341 23744 1.589 .629 .596 .839 .613 3.092 52 309 .591 .97 80 1760 7320 36 44 32 40 0 6458 118 6340 .563 8054 7935 1.775 .533 -.828 -.907
2 11056 6780 97 138 10959 6642 15233 8608 107 159 15136 8469 0 0 6724 3837 42 116 100 98 96 96 17601 23605 1.65 .606 .56 .758 .619 3.135 52 281 .583 .97 80 1910 7320 36 44 47 55 0 6067 123 5944 .542 7703 7578 1.844 .501 -.883 -.998
3 23845 21382 112 153 23732 21229 25049 21507 141 173 24937 21354 0 0 5614 3121 122 121 100 100 100 100 44961 46291 1.118 .895 .856 .932 .874 1.646 32 224 .851 .97 70 2060 7320 36 43 62 69 0 19133 137 18997 .8 19245 19108 1.249 .766 -.321 -.384
4 13891 8877 107 147 13783 8729 15648 9906 134 176 15541 9759 0 0 5283 2681 113 132 100 100 100 100 22512 25300 1.579 .633 .628 .698 .62 1.989 52 293 .599 .97 80 2210 7330 37 45 77 85 0 7943 132 7811 .567 8864 8733 1.765 .562 -.819 -.832
5 950 291 103 142 847 149 978 280 115 157 875 138 0 0 187 92 48 82 100 78 100 34 996 1013 5.685 .176 .158 .164 .17 2.046 32 215 .164 .58 70 2370 7330 37 44 93 100 0 260 127 133 .157 251 123 6.353 .141 -2.667 -2.825
6 8268 6298 156 184 8112 6113 10792 8255 174 203 10636 8070 0 0 4819 3655 85 101 100 100 97 98 14225 18706 1.327 .754 .759 .82 .756 2.398 80 344 .742 .97 100 2520 7340 37 47 107 117 0 5636 165 5470 .674 7387 7221 1.483 .679 -.568 -.559
7 277 133 136 170 141 -37 279 126 152 189 143 -44 0 0 98 49 82 99 69 0 42 0 104 99 null null null .209 .197 5.945 52 310 .209 .12 90 2670 7330 36 45 122 131 -50 119 152 -33 null 113 -39 null null null null
8 21543 18689 112 164 21430 18525 26319 22174 122 180 26206 22010 0 0 9373 7224 53 93 100 100 100 100 39955 48216 1.157 .864 .84 1.05 .864 2.833 52 272 .835 .97 80 2820 7320 36 44 138 146 0 16724 147 16577 .774 19842 19695 1.293 .752 -.37 -.412
9 185 223 104 147 80 75 186 168 113 167 81 20 0 0 55 249 44 100 69 23 46 5 155 101 1.067 .938 .247 .898 .932 3.702 52 291 3.801 .36 90 2970 7320 35 44 152 161 -50 200 132 67 .839 150 18 1.192 .221 -.253 -2.178
10 184 230 97 139 87 90 177 224 101 157 79 84 0 0 57 94 33 92 90 46 61 15 177 163 .967 1.034 1.063 1.216 1.175 3.443 52 292 3.625 .37 80 3120 7320 36 44 168 176 0 206 124 81 .926 200 75 1.08 .951 -.111 -.072
11 1109 1680 100 145 1008 1534 1117 1753 107 158 1016 1607 0 0 166 352 33 75 100 100 100 100 2542 2623 .657 1.522 1.582 1.492 1.536 1.603 32 227 1.643 .94 70 3280 7320 36 43 184 191 0 1503 130 1373 1.362 1569 1438 .734 1.415 .446 .501
12 497 1213 99 145 397 1068 491 1244 108 162 391 1098 0 0 84 395 41 95 100 98 100 98 1465 1489 .372 2.69 2.808 2.578 2.679 1.835 52 259 3.099 .89 80 3430 7320 36 44 199 207 0 1085 130 956 2.407 1113 983 .415 2.513 1.267 1.329
13 421 232 98 150 322 81 436 214 114 186 337 63 0 0 147 91 66 154 94 21 82 0 403 400 3.975 .252 .187 .24 .219 2.885 52 255 .332 .38 80 3570 7320 36 44 213 221 0 208 134 72 .225 191 56 4.442 .167 -2.151 -2.58
14 288 312 98 157 190 155 287 306 104 173 189 148 0 0 122 121 39 83 90 71 84 40 345 337 1.226 .816 .783 .785 .844 3.52 32 176 1.055 .65 60 3720 7300 35 41 229 235 0 279 140 139 .73 274 132 1.37 .701 -.454 -.513
15 125 70 99 146 25 -75 124 59 110 182 24 -86 0 0 34 40 56 305 13 0 1 0 -50 -62 null null null 3.211 3.698 4.918 52 335 -19.239 -.09 90 3870 7310 34 43 242 251 -50 63 131 -67 null 53 -77 null null null null
16 3487 1966 96 145 3391 1821 4034 2118 107 161 3937 1973 0 0 1226 561 50 81 100 100 98 100 5212 5910 1.862 .537 .501 .595 .528 2.316 52 261 .5 .94 80 4020 7320 36 44 258 266 0 1759 130 1630 .481 1895 1766 2.081 .448 -1.057 -1.157
17 151 148 98 151 53 -3 150 134 107 162 52 -17 0 0 50 61 53 79 50 15 13 0 50 35 null null null 1.795 1.963 3.963 52 309 5.248 .47 90 4170 7310 34 43 272 281 -50 132 135 -3 null 120 -15 null null null null
18 117 64 99 148 17 -83 120 55 113 168 20 -93 0 0 26 35 65 149 1 0 0 0 -66 -73 null null null 5.223 3.551 3.9 52 319 -1 -1 90 4320 7310 34 43 287 296 -50 57 132 -74 null 49 -83 null null null null
19 768 638 103 140 664 497 787 636 118 166 683 495 0 0 200 184 69 127 100 96 100 92 1161 1178 1.336 .748 .725 .719 .759 2.125 52 284 .724 .84 80 4480 7310 35 43 304 312 0 571 125 445 .67 569 443 1.493 .649 -.578 -.625
20 3034 4105 98 147 2935 3957 3361 4847 113 194 3262 4699 0 0 1113 1667 59 300 100 98 98 94 6892 7961 .742 1.348 1.441 1.337 1.347 2.001 52 257 1.395 .95 80 4630 7320 36 44 319 327 0 3673 132 3541 1.206 4337 4205 .829 1.289 .271 .366

Total number of rows: 44544

Table truncated, full table size 9764 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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