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Sample GSM989783 Query DataSets for GSM989783
Status Public on Aug 23, 2012
Title PC 389T
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 389T2
Organism Homo sapiens
Characteristics ethnicity: Hispanic
age: 66
pre-operation treatment: None
individual: PC 205T
disease free survival: 16.87
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/2008-09/81287.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 6291 6887 77 59 6214 6827 7264 7125 84 69 7187 7065 0 0 3705 2459 60 63 96 100 92 100 13041 14252 .91 1.099 .983 1.745 .962 6.715 80 449 .911 .86 100 1790 7340 29 39 34 44 0 6270 54 6215 1 6487 6432 1 .895 0 -.16
2 7044 6783 88 67 6956 6715 7503 6735 95 81 7415 6668 0 0 2402 1539 36 66 100 100 100 100 13671 14083 1.036 .965 .899 1.031 .896 2.447 52 275 .903 .87 90 1930 7340 29 38 48 57 0 6175 61 6113 .879 6132 6071 1.138 .819 -.186 -.289
3 11605 27207 93 77 11512 27129 13428 29622 102 92 13335 29545 0 0 6170 9523 38 69 98 100 96 100 38641 42880 .424 2.357 2.216 3.163 2.158 6.85 80 375 2.24 .9 110 2100 7340 28 39 64 75 0 24769 70 24698 2.145 26968 26898 .466 2.017 1.101 1.012
4 6506 6145 88 81 6418 6064 6961 6484 100 89 6873 6402 0 0 2334 2129 44 47 100 98 97 98 12482 13275 1.058 .945 .931 .986 .889 2.92 80 314 .917 .9 110 2240 7350 29 40 78 89 0 5594 74 5521 .86 5903 5828 1.163 .848 -.217 -.238
5 628 318 102 86 525 231 612 324 119 97 509 237 0 0 196 128 74 61 100 92 96 78 756 746 2.273 .44 .466 .39 .458 3.532 52 290 .393 .68 90 2380 7330 28 37 93 102 0 290 78 210 .401 295 216 2.496 .424 -1.32 -1.238
6 6880 8787 107 99 6772 8688 7148 8611 122 119 7040 8511 0 0 2551 2174 68 162 100 100 98 100 15460 15551 .779 1.283 1.209 1.465 1.208 3.249 80 386 1.23 .91 110 2530 7340 28 39 107 118 0 8000 90 7910 1.168 7840 7748 .856 1.101 .224 .138
7 231 223 86 86 145 137 229 207 96 111 143 120 0 0 73 87 46 198 93 18 78 1 282 263 1.058 .945 .839 .817 .858 4.082 80 242 .846 .57 100 2690 7350 30 40 124 134 0 203 78 125 .86 188 109 1.163 .764 -.217 -.388
8 14288 30658 84 96 14203 30561 15073 30657 93 128 14988 30560 0 0 4567 6206 55 284 100 100 100 100 44764 45548 .465 2.152 2.039 2.304 2.01 2.508 80 336 2.17 .9 110 2830 7340 28 39 137 148 0 27911 87 27823 1.959 27910 27822 .51 1.856 .97 .892
9 275 217 84 90 191 127 277 203 92 120 192 113 0 0 85 106 54 277 97 8 82 0 318 305 1.504 .665 .589 .673 .663 4.186 80 360 1.119 .44 110 2990 7350 29 40 153 164 0 198 82 116 .605 185 103 1.652 .536 -.724 -.9
10 324 466 80 83 243 382 280 371 90 97 199 287 0 0 374 466 53 67 85 98 78 91 625 486 .636 1.572 1.442 2.018 1.656 4.603 80 320 1.266 .79 110 3140 7340 28 39 168 179 0 424 76 348 1.431 338 261 .699 1.313 .517 .393
11 840 1340 74 78 765 1261 808 1265 84 92 733 1186 0 0 309 529 57 69 98 100 98 100 2026 1919 .607 1.648 1.618 1.685 1.506 3.075 80 255 1.743 .79 110 3290 7350 29 40 183 194 0 1220 71 1148 1.501 1152 1080 .666 1.473 .586 .559
12 519 1956 70 81 448 1875 584 1712 76 92 514 1630 0 0 278 1046 31 68 89 100 85 100 2323 2144 .239 4.185 3.171 4.504 3.488 4.399 120 367 4.774 .8 120 3440 7340 28 40 198 210 0 1781 74 1707 3.81 1559 1484 .262 2.887 1.93 1.53
13 477 396 71 77 405 319 459 366 73 86 387 288 0 0 158 133 25 48 100 100 100 98 724 675 1.27 .788 .744 .788 .754 2.888 80 289 .696 .69 110 3590 7340 28 39 213 224 0 361 70 290 .717 333 262 1.395 .678 -.48 -.562
14 304 535 64 71 239 464 302 511 69 78 238 440 0 0 80 145 25 43 98 100 96 100 703 678 .515 1.941 1.849 2.01 1.915 2.773 80 272 2.176 .77 110 3740 7340 28 39 228 239 0 487 65 422 1.767 465 401 .566 1.683 .822 .751
15 126 67 73 80 52 -12 113 54 80 87 40 -25 0 0 51 40 36 53 54 10 30 0 40 15 null null null .551 .571 7.108 120 315 .163 .1 120 3890 7340 28 40 243 255 -100 61 73 -11 null 49 -23 null null null null
16 1341 1917 84 68 1256 1848 1511 1940 91 80 1427 1871 0 0 899 871 36 49 87 97 78 95 3104 3298 .68 1.471 1.311 2.235 1.284 6.065 120 387 1.211 .82 120 4040 7340 28 40 258 270 0 1745 62 1682 1.34 1766 1703 .747 1.194 .422 .255
17 230 225 94 72 135 152 214 213 103 80 120 141 0 0 66 87 43 41 98 90 77 80 287 261 .888 1.126 1.175 1.13 1.163 3.17 80 321 .971 .53 110 4200 7340 28 39 274 285 0 205 66 138 1.025 194 128 .976 1.07 .036 .097
18 124 72 102 76 22 -3 113 54 110 86 11 -21 0 0 53 61 43 53 30 12 11 1 19 -10 null null null 1.514 1.586 5.894 120 369 5.881 .1 120 4340 7340 28 40 288 300 -100 66 69 -3 null 49 -19 null null null null
19 578 658 102 89 475 569 539 610 109 96 436 521 0 0 224 248 44 53 100 100 98 100 1044 957 .835 1.198 1.195 1.25 1.119 2.867 80 253 1.164 .67 110 4490 7340 28 39 303 314 0 599 81 518 1.091 555 474 .917 1.088 .125 .122
20 2091 9855 99 90 1991 9764 2322 10281 108 99 2222 10191 0 0 1268 3905 55 54 90 100 82 99 11755 12413 .204 4.904 4.586 7.382 4.416 6.047 120 345 4.784 .87 120 4640 7340 28 40 318 330 0 8972 82 8889 4.465 9360 9278 .224 4.176 2.159 2.062

Total number of rows: 44544

Table truncated, full table size 9597 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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