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Sample GSM989809 Query DataSets for GSM989809
Status Public on Aug 23, 2012
Title PC 188N
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 188N2
Organism Homo sapiens
Characteristics individual: PC 188N
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/2008-08/81104.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 3234 4995 93 172 3140 4822 3114 4892 105 226 3021 4719 0 0 955 978 69 214 100 100 100 100 7962 7740 .651 1.536 1.562 1.584 1.513 2.729 32 234 1.471 .95 70 1920 6990 43 50 36 43 0 4277 147 4129 1.315 4189 4041 .76 1.338 .395 .42
2 2003 2965 93 186 1909 2779 2124 2512 111 242 2030 2325 0 0 1639 2325 68 209 82 78 75 73 4688 4355 .687 1.456 1.145 1.633 1.482 4.511 52 288 1.414 .96 80 2080 6990 43 51 52 60 0 2539 159 2380 1.246 2151 1991 .802 .981 .318 -.028
3 6099 6167 98 190 6001 5976 6598 6577 110 233 6499 6386 0 0 2244 1734 44 153 100 100 100 100 11977 12885 1.004 .996 .983 1.103 .992 3.316 32 170 .935 .95 60 2220 6990 44 50 67 73 0 5281 163 5117 .853 5632 5468 1.173 .841 -.23 -.249
4 4811 7681 100 195 4711 7486 5150 7889 154 317 5050 7694 0 0 1449 1661 254 660 100 100 100 100 12197 12744 .629 1.589 1.524 1.681 1.565 2.661 32 221 1.502 .97 70 2370 6990 43 50 81 88 0 6577 167 6410 1.361 6755 6588 .735 1.305 .444 .384
5 210 155 106 174 104 -18 213 134 137 249 107 -39 0 0 99 78 147 301 34 0 0 0 86 68 null null null .961 1.001 12.533 52 296 1.065 .29 90 2520 6990 42 51 95 104 -50 133 149 -15 null 115 -33 null null null null
6 4038 3074 123 179 3915 2894 4181 3175 140 210 4058 2995 0 0 991 699 88 147 100 100 100 100 6809 7053 1.353 .739 .738 .757 .753 2.564 32 202 .685 .95 70 2670 6990 43 50 111 118 0 2632 153 2478 .633 2719 2565 1.58 .632 -.66 -.662
7 137 141 93 165 43 -23 121 106 111 200 27 -58 0 0 56 136 79 221 26 5 3 1 20 -31 null null null 3.118 2.045 15.432 52 304 3.843 .38 90 2820 6990 42 51 125 134 -50 121 141 -20 null 91 -50 null null null null
8 6252 5947 85 160 6167 5787 6998 6867 100 195 6912 6707 0 0 3658 3645 54 164 100 96 100 93 11954 13619 1.066 .938 .97 .859 .932 2.828 32 202 .937 .97 70 2980 6990 43 50 142 149 0 5092 137 4955 .804 5880 5743 1.245 .831 -.316 -.267
9 70 122 86 150 -16 -28 65 105 98 202 -21 -44 0 0 23 81 49 189 1 3 0 0 -44 -65 null null null 2.542 2.996 6.791 52 295 5.334 .64 90 3120 6980 41 50 155 164 -50 104 128 -24 null 90 -38 null null null null
10 121 161 93 176 27 -15 113 153 101 216 19 -23 0 0 37 77 41 161 36 1 11 0 12 -4 null null null 1.734 1.341 7.881 52 291 5.953 .5 90 3270 6980 41 50 170 179 -50 138 151 -13 null 131 -20 null null null null
11 164 273 95 183 69 89 155 256 107 226 60 73 0 0 80 126 46 151 55 30 38 3 158 133 .775 1.29 1.217 1.577 1.49 5.346 52 295 3.407 .56 90 3420 6980 41 50 185 194 -50 234 157 76 1.104 219 63 .905 1.042 .143 .059
12 208 484 118 269 90 214 196 439 141 327 78 169 0 0 72 287 86 238 50 34 12 12 304 247 .421 2.378 2.167 1.948 2.9 7.797 32 171 4.453 .62 60 3560 6970 42 48 201 207 0 414 230 183 2.036 376 145 .491 1.855 1.026 .892
13 164 221 138 322 25 -101 162 202 160 429 23 -120 0 0 44 137 93 387 7 0 0 0 -76 -97 null null null 6.051 6.377 3.917 52 319 5.7 .59 90 3730 6980 41 50 216 225 -50 189 276 -86 null 173 -103 null null null null
14 190 290 112 245 78 44 178 175 135 356 65 -70 0 0 108 450 83 342 40 7 3 3 122 -5 1.773 .564 null 3.186 3.623 10.218 52 291 5.404 .67 90 3880 6980 41 50 231 240 -50 248 210 38 .483 150 -60 2.07 null -1.05 null
15 106 179 103 199 2 -19 87 96 123 275 -16 -102 0 0 100 455 79 292 5 1 3 1 -17 -118 null null null 3.704 3.387 6.903 52 302 5.34 .63 90 4030 6980 41 50 246 255 -50 153 170 -16 null 82 -87 null null null null
16 925 709 98 196 826 512 897 678 111 230 798 481 0 0 187 213 58 169 100 100 100 81 1338 1279 1.613 .62 .603 .589 .623 3.063 32 202 .706 .72 70 4190 6980 42 49 263 270 0 607 168 438 .531 581 412 1.884 .516 -.914 -.954
17 103 146 102 198 0 -51 96 122 123 265 -6 -75 0 0 32 95 83 231 1 1 0 0 -51 -81 null null null 3.905 4.163 5.142 52 276 3.403 .72 90 4330 6980 41 50 276 285 -50 125 170 -44 null 104 -64 null null null null
18 112 179 106 210 5 -30 74 101 122 262 -32 -109 0 0 179 337 61 186 5 3 3 3 -25 -141 null null null 3.034 3.358 4.695 52 272 2.344 .8 90 4480 6980 41 50 291 300 -50 153 180 -26 null 86 -93 null null null null
19 151 181 104 207 46 -26 140 165 123 262 36 -42 0 0 66 98 100 238 17 1 3 0 20 -6 null null null 1.601 1.539 6.232 52 319 13.95 .24 90 4630 6980 41 50 306 315 -50 155 177 -22 null 141 -36 null null null null
20 766 1578 101 188 665 1390 787 1723 113 241 686 1534 0 0 278 550 59 210 93 100 93 93 2055 2220 .478 2.09 2.236 2.284 2.064 3.818 32 211 2.086 .92 70 4790 6980 42 49 323 330 0 1351 161 1190 1.79 1475 1314 .559 1.915 .84 .937

Total number of rows: 44544

Table truncated, full table size 9619 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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