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Sample GSM989714 Query DataSets for GSM989714
Status Public on Aug 23, 2012
Title PC 99N
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 99N2
Organism Homo sapiens
Characteristics individual: PC 99N
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/2008-08/81079.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 31180 21675 87 52 31093 21623 37452 23950 93 60 37365 23897 0 0 15171 9354 32 31 100 100 100 100 52716 61262 1.438 .695 .64 .816 .708 1.513 32 230 .675 .97 70 1820 7510 23 30 46 53 0 19811 48 19763 .636 21890 21842 1.573 .585 -.654 -.775
2 17748 12328 86 54 17662 12274 7712 3742 92 65 7626 3688 0 0 19786 13943 35 51 96 88 82 80 29936 11314 1.439 .695 .484 .712 .739 2.062 52 306 .698 .98 80 1970 7510 23 31 61 69 0 11268 49 11218 .635 3420 3371 1.574 .442 -.655 -1.178
3 36737 36954 92 59 36644 36895 41830 49014 100 74 41738 48954 0 3 23784 23325 34 61 100 100 100 96 73539 90692 .993 1.007 1.173 .919 .92 1.48 32 231 1.001 .98 70 2120 7500 22 29 76 83 0 33776 54 33722 .92 44798 44743 1.087 1.072 -.12 .1
4 36181 24835 87 59 36093 24776 44839 31071 98 74 44752 31012 0 0 17209 12161 47 62 100 100 100 96 60869 75764 1.457 .686 .693 .58 .67 1.564 32 236 .688 .99 70 2270 7500 22 29 91 98 0 22699 54 22645 .627 28399 28345 1.594 .633 -.673 -.659
5 1923 459 92 67 1830 391 1887 451 99 70 1794 383 0 0 312 88 32 35 100 100 100 100 2221 2177 4.68 .214 .213 .211 .229 1.186 12 104 .186 .92 50 2420 7500 23 28 107 112 0 420 61 357 .195 412 350 5.121 .195 -2.356 -2.358
6 26747 23646 125 75 26621 23571 35294 29641 141 85 35169 29566 0 0 14593 11802 64 53 100 100 100 100 50192 64735 1.129 .885 .841 .928 .848 1.558 52 295 .865 .98 80 2570 7500 22 30 121 129 0 21612 69 21544 .809 27092 27023 1.236 .768 -.305 -.38
7 493 179 98 66 394 112 498 176 123 95 399 110 0 0 167 66 122 179 90 12 84 0 506 509 3.518 .284 .276 .266 .324 1.666 32 176 .285 .72 60 2720 7500 23 29 137 143 0 164 60 102 .26 161 101 3.849 .252 -1.944 -1.989
8 45474 44586 96 62 45378 44524 53404 53387 113 79 53308 53325 0 21 20516 20009 80 79 100 100 100 100 89902 106633 1.019 .981 1 .944 .954 1.091 32 234 .98 .99 70 2870 7500 22 29 151 158 0 40751 57 40694 .897 48795 48739 1.115 .914 -.157 -.129
9 298 252 77 51 221 200 282 253 86 70 205 201 0 0 64 60 37 53 100 100 100 91 421 406 1.105 .905 .98 .897 .921 1.32 12 104 .898 .8 50 3030 7490 22 27 168 173 0 230 47 183 .827 231 184 1.209 .896 -.274 -.158
10 247 285 80 67 166 217 241 295 96 93 160 227 0 0 72 85 65 144 93 81 62 15 383 387 .765 1.307 1.419 1.287 1.24 1.326 32 169 1.448 .87 60 3180 7500 23 29 183 189 0 260 61 198 1.195 270 207 .837 1.297 .257 .375
11 1348 2097 78 52 1269 2044 1460 2478 83 63 1382 2425 0 0 527 902 26 37 100 100 100 96 3313 3807 .621 1.611 1.755 1.482 1.565 1.241 32 227 1.663 .96 70 3330 7500 22 29 197 204 0 1917 48 1868 1.472 2265 2216 .679 1.604 .558 .681
12 822 4862 80 64 742 4797 929 5294 90 74 848 5229 0 0 276 1552 35 55 100 100 100 100 5539 6077 .155 6.465 6.166 6.674 6.535 1.125 32 176 6.482 .97 60 3480 7500 23 29 213 219 0 4444 58 4384 5.909 4839 4779 .169 5.636 2.563 2.495
13 470 356 85 67 385 288 453 332 96 84 368 265 0 0 346 279 41 72 71 57 63 51 673 633 1.337 .748 .72 .779 .791 2.302 52 327 .828 .9 90 3630 7490 20 29 226 235 -50 325 61 263 .684 303 242 1.463 .658 -.549 -.603
14 288 276 77 54 210 221 171 160 85 67 93 106 0 0 224 250 30 45 61 53 55 51 431 199 .95 1.052 1.14 1.128 1.088 1.652 52 291 1.164 .91 90 3780 7490 20 29 241 250 -50 252 49 202 .962 146 97 1.04 1.042 -.056 .059
15 93 49 75 53 18 -3 91 42 85 64 15 -11 0 0 22 26 42 49 11 5 0 0 15 4 null null null 1.202 1.232 3.139 52 335 2.178 .43 90 3930 7490 20 29 256 265 -50 45 48 -3 null 38 -10 null null null null
16 7146 3770 81 59 7064 3711 8235 4165 90 78 8154 4105 0 0 2629 1296 42 63 100 100 100 100 10775 12259 1.904 .525 .503 .541 .515 1.078 32 230 .52 .98 70 4090 7490 21 28 273 280 0 3446 54 3392 .48 3807 3752 2.083 .46 -1.058 -1.12
17 167 271 80 50 87 221 163 301 93 71 82 250 0 0 78 140 52 58 65 81 34 71 308 332 .394 2.54 3.049 2.263 2.637 2.367 32 175 .924 .44 60 4240 7490 22 28 289 295 0 248 46 202 2.322 275 228 .431 2.787 1.215 1.478
18 93 69 75 54 18 15 88 51 85 65 12 -2 0 0 36 61 34 47 19 13 1 5 33 10 1.2 .833 null 1.273 1.453 3.68 52 333 1.878 .53 90 4390 7490 20 29 302 311 -50 63 49 14 .762 47 -2 1.313 null -.393 null
19 1587 956 75 52 1511 903 1545 930 79 63 1470 877 0 0 274 216 24 40 100 100 100 100 2414 2347 1.673 .598 .597 .591 .57 1.075 32 176 .589 .96 60 4540 7490 22 28 319 325 0 874 48 825 .546 850 802 1.831 .545 -.872 -.875
20 5104 9886 81 57 5022 9829 6522 11600 97 78 6440 11543 0 0 2441 4192 123 173 100 100 100 100 14851 17983 .511 1.957 1.792 2.09 1.938 1.253 32 221 1.92 .98 70 4690 7500 22 29 333 340 0 9036 52 8984 1.789 10602 10550 .559 1.638 .839 .712

Total number of rows: 44544

Table truncated, full table size 9419 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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