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Sample GSM989701 Query DataSets for GSM989701
Status Public on Aug 23, 2012
Title PC 26T
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 26T2.0
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 43
pre-operation treatment: None
individual: PC 15T
disease free survival: 90.23
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/2008-09/81308.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 10259 10450 55 60 10204 10389 10412 10467 58 73 10357 10406 0 0 1336 1280 22 48 100 100 100 100 20593 20763 .982 1.018 1.005 1.02 1.01 1.698 52 376 .98 .93 90 1820 7020 21 30 25 34 0 8990 52 8937 .876 9004 8952 1.142 .864 -.191 -.21
2 9545 10404 59 69 9486 10334 11357 11272 63 82 11298 11203 0 0 3722 3371 26 52 100 100 100 100 19820 22501 .918 1.089 .992 1.147 1.048 2.704 52 272 1.009 .87 90 1970 7040 23 32 40 49 0 8950 59 8890 .937 9697 9638 1.067 .853 -.094 -.229
3 8840 12689 55 69 8784 12619 10581 14793 59 82 10525 14724 0 0 3937 5378 18 53 100 100 99 99 21403 25249 .696 1.437 1.399 1.462 1.411 3.588 120 440 1.412 .94 120 2130 7030 21 33 55 67 0 10916 59 10856 1.236 12726 12667 .809 1.203 .306 .267
4 11705 12477 56 70 11649 12406 11969 12613 59 88 11912 12543 0 0 2254 2258 18 95 100 100 100 100 24055 24455 .939 1.065 1.053 1.076 1.076 1.897 80 364 1.026 .92 110 2270 7030 21 32 69 80 0 10734 60 10673 .916 10851 10790 1.091 .906 -.126 -.143
5 506 281 59 70 446 210 480 264 65 88 420 193 0 0 151 127 23 97 100 80 100 48 656 613 2.124 .471 .46 .42 .441 2.899 80 341 .441 .61 110 2430 7040 22 33 85 96 0 242 60 181 .405 227 166 2.469 .395 -1.304 -1.339
6 4168 7360 69 82 4098 7277 4733 8216 91 112 4663 8133 0 0 2544 4369 73 102 97 100 92 99 11375 12796 .563 1.776 1.744 2.035 1.917 3.846 120 376 1.784 .92 120 2580 7050 23 35 100 112 0 6332 71 6260 1.528 7068 6997 .655 1.5 .611 .585
7 190 211 65 88 124 123 179 213 90 112 114 124 0 0 49 95 77 97 80 55 21 25 247 238 1.008 .992 1.088 .872 1.079 4.368 52 232 1.377 .47 80 2720 7020 22 30 116 124 0 182 76 106 .853 183 107 1.172 .936 -.229 -.096
8 11151 16323 57 73 11094 16250 11677 16360 59 86 11619 16287 0 0 2778 2932 18 81 100 100 100 100 27344 27906 .683 1.465 1.402 1.516 1.448 1.925 80 383 1.383 .94 110 2870 7030 21 32 129 140 0 14042 63 13979 1.26 14074 14011 .794 1.206 .334 .27
9 146 166 53 63 93 103 143 152 55 76 90 88 0 0 45 87 16 79 97 52 96 22 196 178 .903 1.108 .978 .99 1.015 4.833 80 385 2.188 .46 110 3030 7020 20 31 145 156 0 143 54 89 .953 131 76 1.05 .841 -.07 -.25
10 201 200 51 48 150 152 199 204 54 60 147 155 0 0 59 97 16 38 98 86 98 72 302 302 .987 1.013 1.054 .944 1.096 3.177 80 336 1.197 .62 110 3190 7040 22 33 161 172 0 172 41 131 .872 175 133 1.147 .907 -.198 -.141
11 415 799 51 51 363 747 418 752 54 65 366 701 0 0 115 257 15 42 100 100 100 100 1110 1067 .486 2.058 1.915 2.049 2.056 2.168 80 261 2.086 .88 100 3330 7050 24 34 176 186 0 687 44 643 1.77 647 603 .565 1.648 .824 .72
12 439 615 50 58 389 556 432 595 53 68 382 537 0 0 128 226 14 45 100 100 100 100 945 919 .7 1.429 1.406 1.392 1.468 2.544 80 325 1.433 .79 110 3480 7040 22 33 190 201 0 529 50 478 1.23 512 462 .813 1.209 .298 .274
13 378 362 50 54 327 308 382 358 52 65 331 303 0 0 96 158 13 41 100 98 100 92 635 634 1.062 .942 .915 .825 .931 3.135 80 276 .948 .75 100 3640 7040 23 33 207 217 0 311 46 265 .81 308 261 1.234 .787 -.303 -.345
14 210 225 52 54 158 170 206 203 63 70 154 148 0 0 126 142 41 48 77 78 68 67 328 302 .929 1.076 .961 1.08 1.052 3.689 120 346 .971 .69 120 3790 7030 21 33 221 233 0 194 46 146 .926 175 127 1.08 .827 -.112 -.274
15 118 88 50 54 67 34 79 56 58 69 28 1 0 0 111 96 35 47 40 25 20 15 101 29 1.971 .507 .036 .894 .905 6.173 120 337 .631 .5 120 3940 7020 20 32 236 248 -100 76 46 29 .437 48 1 2.291 .031 -1.196 -5.024
16 1224 1397 50 64 1174 1332 1174 1399 53 74 1123 1334 0 0 237 289 17 46 100 100 100 100 2506 2457 .881 1.135 1.188 1.134 1.142 1.933 80 299 1.115 .91 110 4090 7020 20 31 251 262 0 1202 55 1146 .976 1204 1148 1.025 1.022 -.035 .031
17 119 113 50 59 68 53 118 109 54 69 67 49 0 0 33 53 18 45 93 55 86 16 121 116 1.283 .779 .731 .837 .931 4.856 80 223 1.082 .27 110 4240 7050 23 34 266 277 0 97 51 46 .671 94 42 1.491 .629 -.577 -.669
18 65 54 48 53 17 1 63 51 50 64 14 -2 0 0 19 29 13 42 50 8 28 0 18 12 17 .059 null 1.371 1.426 5.416 120 346 -1 -1 120 4390 7040 22 34 281 293 -100 46 46 1 .051 44 -2 19.761 null -4.305 null
19 553 710 49 53 504 656 568 645 51 64 518 591 0 0 163 244 13 40 100 100 100 100 1160 1109 .768 1.302 1.141 1.287 1.246 2.325 80 273 1.218 .83 100 4540 7040 23 33 297 307 0 611 46 564 1.12 555 508 .893 .982 .163 -.027
20 2262 9629 50 57 2212 9572 2298 9695 52 74 2248 9638 0 0 519 1640 13 91 100 100 100 100 11784 11886 .231 4.327 4.287 4.424 4.305 1.837 80 336 4.459 .92 110 4690 7030 21 32 311 322 0 8284 49 8234 3.723 8340 8291 .269 3.688 1.896 1.883

Total number of rows: 44544

Table truncated, full table size 9404 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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