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Sample GSM989705 Query DataSets for GSM989705
Status Public on Aug 23, 2012
Title PC 538N
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 538N2
Organism Homo sapiens
Characteristics individual: PC 538N
disease state: Normal
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/2008-08/81163.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 18403 24037 92 114 18311 23923 18926 25958 103 130 18833 25843 0 0 4107 5813 47 88 100 100 100 100 42234 44676 .765 1.306 1.372 1.302 1.329 1.303 52 385 1.316 .97 90 1810 6970 16 25 28 37 0 22806 108 22698 1.24 24629 24520 .807 1.302 .31 .381
2 17032 21590 102 123 16929 21467 19546 26342 112 139 19444 26219 0 0 5234 9205 46 73 100 100 100 100 38396 45663 .789 1.268 1.348 1.149 1.329 1.763 52 292 1.349 .96 80 1970 6960 16 24 45 53 0 20484 117 20368 1.203 24993 24876 .831 1.279 .267 .355
3 23618 20481 132 131 23486 20350 26328 22052 139 146 26195 21921 0 0 7734 5594 51 82 100 100 100 100 43836 48116 1.154 .866 .837 .91 .834 1.43 52 254 .829 .97 80 2110 6980 18 26 59 67 0 19432 124 19308 .822 20923 20798 1.216 .794 -.283 -.333
4 18431 22975 124 139 18307 22836 18983 24595 129 151 18859 24456 0 0 3706 6545 45 65 100 100 100 100 41143 43315 .802 1.247 1.297 1.182 1.284 1.31 52 294 1.275 .97 90 2280 6980 17 26 75 84 0 21799 132 21667 1.184 23336 23204 .845 1.23 .243 .299
5 967 189 121 141 845 48 994 184 140 161 872 43 0 0 244 55 95 111 98 7 96 1 893 915 17.604 .057 .049 .06 .085 2.809 52 228 .055 .3 80 2430 6980 18 26 91 99 0 179 134 46 .054 175 41 18.554 .047 -4.214 -4.418
6 13613 13361 184 172 13428 13188 12970 13145 214 193 12785 12973 0 0 2138 1724 150 119 100 100 100 100 26616 25758 1.018 .982 1.015 .986 .989 1.089 52 262 .977 .97 90 2570 6980 17 26 104 113 0 12677 163 12513 .932 12472 12309 1.073 .963 -.102 -.055
7 335 138 165 159 169 -21 346 134 196 189 180 -25 0 0 80 55 161 217 55 0 1 0 148 155 null null null .213 .164 3.866 52 299 .351 .37 90 2720 6980 17 26 119 128 -50 131 151 -20 null 127 -24 null null null null
8 26030 20896 153 138 25876 20758 27503 21780 168 157 27349 21642 0 0 7251 4578 78 84 100 100 100 100 46634 48991 1.247 .802 .791 .847 .789 1.519 52 287 .773 .98 90 2870 6990 18 27 134 143 0 19826 131 19695 .761 20665 20534 1.314 .751 -.394 -.413
9 123 118 121 132 1 -14 122 107 129 149 0 -25 0 0 29 53 51 76 9 5 0 1 -13 -25 null null null 1.722 1.505 3.443 52 317 4.286 .25 90 3020 6960 15 24 149 158 -50 112 125 -13 null 102 -24 null null null null
10 125 251 104 125 20 126 122 245 115 148 17 120 0 0 33 74 49 89 15 73 5 25 146 137 .159 6.3 7.059 4.946 5.056 3.896 52 309 5.011 .35 90 3170 6960 15 24 164 173 -50 238 119 120 5.977 232 114 .167 6.697 2.58 2.744
11 515 686 102 117 412 568 514 705 110 134 411 588 0 0 196 231 46 78 96 98 90 94 980 999 .725 1.379 1.431 1.497 1.511 1.665 52 262 1.388 .88 80 3320 6970 17 25 180 188 0 651 111 539 1.308 669 558 .764 1.357 .387 .441
12 254 704 104 126 149 578 246 712 113 143 141 586 0 0 61 181 48 71 96 100 80 100 727 727 .258 3.879 4.156 3.984 4.023 1.549 52 320 4.053 .79 90 3480 6960 15 24 195 204 0 668 120 548 3.681 676 556 .272 3.943 1.88 1.979
13 223 231 102 124 120 107 234 231 114 144 131 107 0 0 71 88 61 89 76 55 59 21 227 238 1.121 .892 .817 .869 .913 2.392 52 326 1.353 .71 90 3630 6950 14 23 210 219 -50 219 118 102 .846 219 102 1.182 .775 -.241 -.368
14 198 180 103 120 94 60 202 166 112 143 98 46 0 0 70 79 50 87 69 30 44 5 154 144 1.567 .638 .469 .547 .487 3.012 52 264 1.854 .46 80 3780 6950 15 23 226 234 0 171 114 57 .606 157 44 1.651 .445 -.724 -1.167
15 97 52 104 132 -6 -80 93 49 113 154 -10 -83 0 0 24 26 44 83 3 0 0 0 -86 -93 null null null 4.573 4.514 2.497 52 286 4.137 .42 90 3920 6960 15 24 239 248 -50 49 125 -76 null 46 -79 null null null null
16 2786 1269 101 125 2684 1143 2802 1284 110 142 2700 1159 0 0 389 262 43 72 100 100 100 100 3827 3859 2.348 .426 .429 .419 .424 1.221 52 214 .426 .95 80 4070 6980 18 26 255 263 0 1204 119 1084 .404 1218 1100 2.475 .407 -1.307 -1.296
17 120 113 97 128 22 -15 114 103 117 175 16 -25 0 0 33 55 105 389 1 0 0 0 7 -9 null null null 2.226 2.527 3.479 52 292 2.056 .6 90 4220 6960 15 24 269 278 -50 107 121 -14 null 98 -24 null null null null
18 91 64 96 125 -4 -61 85 52 113 159 -10 -73 0 0 28 39 65 166 1 0 0 0 -65 -83 null null null 3.553 3.303 2.466 52 291 3.393 .73 90 4370 6960 15 24 284 293 -50 61 119 -58 null 49 -69 null null null null
19 508 344 104 128 403 216 507 319 128 167 402 191 0 0 152 114 139 203 98 42 76 7 619 593 1.866 .536 .475 .513 .523 2.656 52 329 .608 .64 90 4520 6950 14 23 299 308 0 326 121 205 .509 303 181 1.966 .451 -.976 -1.149
20 2010 3630 112 136 1897 3494 2171 3813 126 165 2058 3677 0 0 536 1194 68 109 100 100 100 100 5391 5735 .543 1.842 1.787 1.759 1.861 1.488 52 281 1.917 .95 80 4670 6950 15 23 315 323 0 3444 129 3315 1.748 3618 3489 .572 1.695 .805 .761

Total number of rows: 44544

Table truncated, full table size 9676 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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