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Sample GSM989766 Query DataSets for GSM989766
Status Public on Aug 23, 2012
Title PC 186T
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 PT 186
Organism Homo sapiens
Characteristics individual: PC 186T
disease state: Tumor
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/2008-11/81781.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 GPL15972
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 6037 5094 40 54 5996 5040 6463 5817 44 64 6422 5763 0 0 1510 1999 17 54 100 100 100 100 11036 12185 1.19 .841 .897 .724 .894 2.755 52 376 .865 .95 90 1580 7630 26 35 37 46 0 4142 44 4098 .683 4730 4686 1.463 .73 -.549 -.455
2 5385 4492 40 49 5344 4442 6120 5342 43 59 6079 5292 0 0 2177 2210 10 39 100 100 100 100 9786 11371 1.203 .831 .871 .727 .857 2.449 52 251 .852 .96 80 1730 7640 28 36 53 61 0 3653 40 3612 .676 4344 4303 1.48 .708 -.565 -.498
3 3370 7217 41 55 3328 7162 3539 8168 47 63 3497 8113 0 0 736 2631 44 43 100 100 100 100 10490 11610 .465 2.152 2.32 2.025 2.344 2.17 52 253 2.341 .94 80 1880 7630 27 35 68 76 0 5868 45 5824 1.75 6642 6597 .571 1.886 .807 .916
4 5771 4990 42 55 5729 4934 6181 5773 47 73 6139 5717 0 0 1592 1853 22 106 100 100 100 100 10663 11856 1.161 .861 .931 .83 .915 2.239 52 272 .871 .94 80 2030 7630 27 35 83 91 0 4058 45 4012 .7 4694 4649 1.428 .757 -.514 -.401
5 169 113 44 55 125 58 164 106 47 63 120 51 0 0 31 44 17 32 100 65 100 37 183 171 2.155 .464 .425 .435 .431 3.201 32 228 .347 .41 70 2180 7630 27 34 98 105 0 92 45 47 .377 86 41 2.65 .346 -1.406 -1.533
6 1460 1363 51 65 1408 1297 1510 1518 57 77 1458 1452 0 0 336 509 22 44 100 100 100 100 2705 2910 1.086 .921 .996 .833 .92 2.204 52 317 .937 .93 90 2340 7630 26 35 113 122 0 1108 53 1055 .749 1234 1181 1.335 .81 -.417 -.304
7 104 92 43 57 61 35 101 81 59 77 57 23 0 0 22 45 143 108 0 11 0 0 96 80 1.743 .574 .404 .544 .662 4.422 52 253 1.387 .44 80 2490 7630 27 35 129 137 0 75 46 28 .467 66 19 2.143 .328 -1.1 -1.608
8 2911 6067 42 61 2869 6006 3069 6489 55 81 3026 6428 0 0 710 2354 127 99 100 100 100 100 8875 9454 .478 2.093 2.124 1.881 2.26 2.216 52 319 2.231 .95 90 2640 7630 26 35 143 152 0 4933 50 4884 1.702 5276 5227 .587 1.727 .767 .789
9 81 77 48 66 33 10 84 75 51 83 35 8 0 0 12 30 13 58 91 16 83 0 43 43 3.3 .303 .229 .958 1.379 3.131 12 68 1.991 .35 40 2800 7640 30 34 162 166 0 63 54 8 .246 61 7 4.058 .186 -2.021 -2.428
10 93 109 43 62 50 46 93 108 46 76 50 45 0 0 20 46 17 54 93 40 75 12 96 95 1.087 .92 .9 .882 1.213 5.017 32 173 1.861 .38 60 2940 7620 27 33 175 181 0 89 50 37 .748 88 37 1.337 .732 -.419 -.45
11 220 409 41 61 178 348 229 427 45 77 188 366 0 0 53 144 11 115 100 90 100 82 526 554 .511 1.955 1.947 1.76 2.035 2.584 52 278 2.148 .89 80 3090 7620 26 34 189 197 0 333 50 283 1.59 347 298 .629 1.583 .669 .663
12 147 344 41 51 105 292 146 331 44 66 104 279 0 0 30 119 11 119 100 93 100 62 397 383 .36 2.781 2.683 2.645 2.466 2.496 32 230 3.696 .75 70 3240 7620 26 33 204 211 0 280 41 237 2.261 269 227 .442 2.181 1.177 1.125
13 125 110 41 64 83 45 121 118 44 71 80 54 0 0 23 44 14 39 100 56 100 15 128 134 1.844 .542 .675 .567 .683 3.432 32 227 .619 .43 70 3390 7620 26 33 219 226 0 89 52 37 .441 96 44 2.268 .549 -1.182 -.865
14 80 119 40 63 39 56 77 122 44 72 36 58 0 0 16 41 14 50 96 50 71 9 95 94 .696 1.436 1.611 1.365 1.37 3.441 32 202 3.702 .48 70 3550 7620 26 33 235 242 0 97 51 46 1.168 99 47 .856 1.31 .224 .39
15 48 50 40 57 7 -7 45 43 43 64 4 -14 0 0 17 28 13 37 18 2 5 1 0 -10 null null null 3.033 4.365 4.065 80 389 72.08 .03 100 3700 7620 25 35 249 259 -50 41 46 -6 null 35 -11 null null null null
16 181 375 40 61 140 314 184 385 45 76 143 324 0 0 39 143 17 92 100 90 100 78 454 467 .446 2.243 2.266 2.021 2.29 2.607 52 263 2.678 .85 80 3850 7620 26 34 265 273 0 305 50 255 1.824 313 263 .548 1.842 .867 .882
17 56 123 45 62 10 61 45 130 52 84 0 68 0 0 25 68 23 125 25 16 16 0 71 68 .164 6.1 null 4.904 3.175 3.942 12 104 13.003 .33 50 3980 7550 20 25 279 284 0 100 50 50 4.96 106 55 .202 null 2.31 null
18 44 51 41 59 2 -8 43 43 47 76 1 -16 0 0 8 34 24 102 2 1 0 1 -6 -15 null null null 3.992 4.067 4.513 80 478 23.359 .08 100 4140 7580 21 31 293 303 -50 41 48 -7 null 35 -13 null null null null
19 109 133 40 57 68 76 105 132 43 65 64 75 0 0 34 43 11 41 96 80 92 36 144 139 .895 1.118 1.172 1.037 1.056 3.453 52 341 1.66 .51 90 4300 7620 25 34 309 318 0 108 46 62 .909 107 61 1.1 .953 -.138 -.07
20 644 3219 41 57 603 3161 661 3705 44 68 620 3647 0 0 141 1165 16 57 100 100 100 100 3764 4267 .191 5.242 5.882 4.628 5.442 2.393 52 312 5.741 .95 90 4460 7610 24 33 325 334 0 2617 46 2570 4.263 3013 2966 .235 4.783 2.092 2.258

Total number of rows: 44544

Table truncated, full table size 9131 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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