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Sample GSM989794 Query DataSets for GSM989794
Status Public on Aug 23, 2012
Title PC 621T
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 621T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 44
individual: PC 166T
disease state: Tumor
pre-operation treatment: None
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/2008-08/81149.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 6473 5206 102 102 6371 5103 6757 5222 106 117 6655 5120 0 0 2069 1290 29 96 100 100 100 100 11474 11775 1.248 .801 .769 .836 .776 1.587 52 316 .772 .98 80 1980 7460 50 58 54 62 0 4979 98 4880 .766 4994 4896 1.306 .736 -.385 -.443
2 6054 4770 110 112 5943 4657 6104 4687 113 120 5993 4574 0 0 1101 588 32 52 100 100 100 100 10600 10567 1.276 .784 .763 .793 .765 1.397 32 224 .77 .98 70 2130 7450 49 56 69 76 0 4562 107 4454 .749 4482 4374 1.334 .73 -.416 -.454
3 8960 8244 113 116 8846 8128 10390 9667 118 126 10277 9551 0 0 3802 3222 35 67 100 100 100 100 16974 19828 1.088 .919 .929 1.028 .927 1.938 52 271 .901 .98 80 2280 7450 49 57 84 92 0 7884 111 7773 .879 9245 9134 1.138 .889 -.187 -.17
4 5165 4277 112 111 5053 4165 5401 4329 119 121 5288 4217 0 0 1380 736 38 55 100 100 100 100 9218 9505 1.213 .824 .797 .867 .79 1.634 52 254 .789 .97 90 2430 7470 50 59 98 107 0 4090 106 3983 .788 4140 4033 1.269 .763 -.343 -.391
5 348 121 109 111 238 9 356 117 114 121 247 5 0 0 200 46 32 54 75 15 71 3 247 252 26.444 .038 .02 .209 .13 8.592 52 272 -.02 -.04 90 2580 7460 49 58 113 122 -50 116 106 9 .036 112 5 27.652 .019 -4.789 -5.691
6 5674 5118 133 125 5540 4993 5936 5276 141 136 5802 5150 0 0 1275 1100 51 79 100 100 100 100 10533 10952 1.11 .901 .888 .902 .89 1.394 52 272 .886 .98 90 2730 7460 49 58 128 137 0 4894 120 4775 .862 5046 4925 1.16 .849 -.214 -.236
7 192 101 120 124 71 -23 195 95 129 132 74 -29 0 0 65 46 49 59 59 5 30 0 48 45 null null null .528 .533 6.362 52 282 -.13 -.04 90 2880 7460 49 58 143 152 -50 97 119 -22 null 91 -28 null null null null
8 9843 8258 118 132 9724 8126 11311 9369 123 138 11192 9237 0 0 3555 3127 37 63 100 100 100 100 17850 20429 1.197 .836 .825 .813 .819 1.435 52 235 .837 .99 80 3040 7460 50 58 160 168 0 7897 126 7771 .799 8960 8833 1.251 .789 -.323 -.341
9 99 90 111 116 -12 -25 96 78 117 124 -14 -37 0 0 26 39 36 60 5 0 0 0 -37 -51 null null null 1.48 1.647 3.18 52 280 2.576 .41 90 3180 7450 48 57 173 182 -50 86 111 -24 null 75 -35 null null null null
10 144 157 113 123 30 33 102 117 122 146 -11 -6 0 0 270 172 58 269 7 3 3 1 63 -17 .909 1.1 null 1.388 1.283 4.268 52 312 .645 .81 90 3330 7450 48 57 188 197 -50 150 118 32 1.052 112 -6 .951 null .073 null
11 265 286 118 133 147 152 263 269 124 138 145 135 0 0 59 79 40 60 96 90 96 65 299 280 .967 1.034 .931 .935 .961 2.477 32 199 1.38 .65 70 3490 7460 50 57 205 212 0 274 127 145 .989 257 129 1.011 .89 -.016 -.168
12 171 261 118 129 53 132 159 258 123 136 41 129 0 0 57 122 39 51 51 69 34 57 185 170 .402 2.491 3.146 2.408 2.202 3.251 52 274 3.37 .5 90 3630 7460 49 58 218 227 -50 250 123 126 2.382 247 123 .42 3.009 1.252 1.589
13 225 139 124 136 101 3 223 135 141 139 98 -1 0 0 52 59 52 68 91 25 41 0 104 97 33.667 .03 null .814 .469 7.615 12 68 .171 .14 40 3770 7460 52 56 235 239 0 133 130 3 .028 129 -1 35.205 null -5.138 null
14 163 164 119 133 43 31 165 162 131 157 45 29 0 0 40 47 82 134 18 0 0 0 74 74 1.387 .721 .644 1.134 .98 2.967 32 176 36.794 .08 60 3940 7430 48 54 251 257 0 157 127 30 .689 155 28 1.45 .616 -.537 -.698
15 98 67 116 135 -17 -67 97 63 127 147 -18 -72 0 0 26 33 101 67 0 0 0 0 -84 -90 null null null 3.023 2.548 2.888 52 315 .521 .57 90 4090 7440 47 56 264 273 -50 64 129 -64 null 60 -69 null null null null
16 1473 589 115 126 1358 462 1526 615 122 133 1411 488 0 0 317 153 39 53 100 98 100 98 1820 1899 2.939 .34 .346 .326 .338 1.694 52 225 .329 .91 80 4240 7450 49 57 280 288 0 563 120 442 .325 588 467 3.074 .331 -1.62 -1.596
17 118 122 112 132 5 -9 115 110 120 137 2 -21 0 0 34 38 40 52 7 3 3 0 -4 -19 null null null 1.053 1.257 6.274 52 272 2.973 .16 90 4390 7450 48 57 294 303 -50 117 126 -9 null 105 -20 null null null null
18 90 73 113 132 -23 -59 89 59 118 137 -24 -73 0 0 21 48 37 60 0 3 0 0 -82 -97 null null null 3.29 2.499 3.006 52 282 3.058 .34 90 4540 7450 48 57 309 318 -50 70 126 -56 null 56 -70 null null null null
19 270 201 114 136 156 64 267 190 120 143 153 53 0 0 78 62 39 54 90 48 82 25 220 206 2.438 .41 .346 .444 .464 2.928 52 283 .67 .44 90 4700 7450 48 57 325 334 0 192 130 61 .392 182 51 2.549 .331 -1.35 -1.594
20 1093 2002 116 142 977 1860 1300 2338 121 153 1183 2196 0 0 526 976 39 116 90 88 86 84 2837 3379 .525 1.904 1.856 1.891 1.903 1.686 52 317 1.922 .97 90 4840 7440 47 56 339 348 0 1915 136 1779 1.821 2236 2100 .549 1.775 .864 .828

Total number of rows: 44544

Table truncated, full table size 9566 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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