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Sample GSM989675 Query DataSets for GSM989675
Status Public on Aug 23, 2012
Title PC 97T
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 97T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 65
pre-operation treatment: None
individual: PC 86T
disease free survival: 69.00
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/2008-08/81117.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 4968 4257 84 74 4883 4182 6107 5069 93 97 6022 4994 0 0 2268 1923 47 151 100 98 100 98 9065 11016 1.168 .856 .829 .838 .835 1.77 52 306 .848 .97 80 1900 6990 39 47 58 66 0 3647 63 3583 .734 4343 4279 1.363 .711 -.447 -.493
2 4438 3657 88 71 4349 3585 5510 4495 97 91 5421 4423 0 0 2237 1959 48 130 98 96 98 92 7934 9844 1.213 .824 .816 .788 .839 2.2 52 288 .831 .97 80 2050 6990 39 47 73 81 0 3133 61 3072 .706 3851 3789 1.416 .699 -.502 -.517
3 4640 6039 90 75 4550 5963 5610 7209 100 89 5520 7133 0 0 1911 2681 70 53 100 100 100 98 10513 12653 .763 1.311 1.292 1.146 1.278 2.007 52 290 1.342 .97 80 2210 6990 39 47 89 97 0 5174 64 5109 1.123 6176 6111 .891 1.107 .167 .147
4 4779 3951 89 76 4689 3874 4956 4035 92 88 4867 3958 0 0 1149 1265 25 51 100 100 100 100 8563 8825 1.21 .826 .813 .779 .814 1.485 52 302 .852 .98 90 2360 6990 38 47 103 112 0 3385 65 3319 .708 3457 3391 1.413 .697 -.498 -.521
5 336 121 103 72 232 48 336 113 109 86 232 41 0 0 104 62 38 52 96 40 90 9 280 273 4.833 .207 .177 .233 .259 4.166 32 196 .213 .38 70 2500 6990 39 46 118 125 0 104 62 41 .177 97 35 5.641 .151 -2.496 -2.723
6 3411 3220 126 95 3285 3124 3532 3337 136 107 3405 3241 0 0 861 1134 50 69 100 100 100 98 6409 6646 1.052 .951 .952 .861 .948 1.625 52 293 .999 .97 90 2650 6990 38 47 132 141 0 2759 81 2677 .815 2859 2777 1.227 .816 -.296 -.294
7 125 87 89 85 36 2 120 81 99 100 31 -4 0 0 35 44 38 65 40 1 11 1 38 27 18 .056 null .816 .89 6.187 52 297 5.882 .36 90 2790 6980 37 46 146 155 -50 75 73 2 .048 69 -3 21.009 null -4.393 null
8 6106 7780 97 87 6008 7692 6043 7873 107 100 5946 7786 0 0 560 1222 39 59 100 100 100 100 13700 13732 .781 1.28 1.309 1.266 1.295 1.235 32 202 1.333 .97 70 2950 6990 39 46 163 170 0 6666 75 6590 1.097 6745 6671 .912 1.122 .133 .166
9 81 76 84 87 -2 -10 79 69 94 101 -4 -17 0 0 21 27 39 67 5 1 0 0 -12 -21 null null null 2.018 2.03 4.198 52 295 2.587 .3 90 3090 6980 37 46 176 185 -50 65 75 -9 null 59 -15 null null null null
10 80 66 80 75 0 -9 77 60 85 86 -3 -15 0 0 19 37 27 50 11 7 0 1 -9 -18 null null null 1.557 1.771 3.17 52 311 3.9 .33 90 3240 6980 37 46 191 200 -50 57 64 -8 null 51 -13 null null null null
11 193 197 80 66 113 131 186 195 85 77 105 129 0 0 40 67 29 44 96 87 90 68 244 234 .863 1.159 1.229 1.056 1.162 2.504 32 173 1.527 .66 60 3400 6980 39 45 209 215 0 169 57 112 .993 167 111 1.007 1.053 -.01 .074
12 139 213 77 83 62 130 137 205 79 89 60 122 0 0 35 76 23 38 86 88 67 75 192 182 .477 2.097 2.033 2.108 2.017 2.765 52 263 2.68 .6 80 3550 6980 38 46 223 231 0 182 71 111 1.796 176 105 .557 1.742 .845 .801
13 112 69 78 72 33 -3 113 64 81 86 34 -8 0 0 36 35 26 68 57 7 32 0 30 26 null null null .816 .74 3.955 52 292 8.609 .04 90 3700 6980 37 46 237 246 -50 59 62 -3 null 55 -7 null null null null
14 115 86 76 73 39 12 112 74 81 86 36 1 0 0 31 49 28 69 57 11 23 3 51 37 3.25 .308 .028 1.05 1.343 7.167 52 292 3.413 .55 90 3850 6980 37 46 252 261 -50 74 63 10 .264 63 1 3.793 .024 -1.923 -5.393
15 76 54 76 77 0 -23 74 49 79 85 -1 -28 0 0 16 24 23 45 7 1 1 0 -23 -29 null null null 3.583 2.894 3.025 52 292 4.965 .31 90 4000 6980 37 46 267 276 -50 46 66 -20 null 42 -24 null null null null
16 710 324 77 73 632 250 739 335 82 86 661 261 0 0 162 100 30 109 100 90 100 67 882 922 2.528 .396 .395 .371 .39 1.718 52 253 .394 .88 80 4150 6980 38 46 283 291 0 278 63 214 .339 287 224 2.951 .338 -1.561 -1.564
17 83 86 79 76 3 9 81 86 83 93 1 9 0 0 18 36 29 78 13 3 0 0 12 10 .333 3 9 1.896 1.852 2.868 52 282 7.873 .19 90 4300 6980 37 46 297 306 -50 74 65 8 2.57 74 8 .389 7.711 1.362 2.947
18 93 70 82 84 10 -13 82 60 85 95 0 -23 0 0 38 40 25 56 17 9 11 0 -3 -23 null null null 2.126 1.569 3.728 52 278 22.714 .05 90 4450 6980 37 46 312 321 -50 60 72 -11 null 51 -20 null null null null
19 161 147 83 75 77 71 164 148 87 92 80 72 0 0 47 62 23 84 87 40 68 6 148 152 1.085 .922 .9 .803 .915 3.215 32 171 5.636 .29 60 4590 6970 38 44 328 334 0 126 64 61 .79 127 62 1.266 .771 -.34 -.375
20 513 1263 79 89 433 1174 563 1370 85 98 483 1281 0 0 169 383 30 61 98 100 98 100 1607 1764 .369 2.711 2.652 2.883 2.736 1.724 52 257 2.751 .94 80 4750 6980 38 46 343 351 0 1082 76 1006 2.323 1174 1098 .43 2.272 1.216 1.184

Total number of rows: 44544

Table truncated, full table size 9287 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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