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Sample GSM989755 Query DataSets for GSM989755
Status Public on Aug 23, 2012
Title PC 593N
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 593N2
Organism Homo sapiens
Characteristics individual: PC 593N
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/2008-08/81147.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 12930 23227 64 159 12865 23068 14479 25268 69 175 14414 25109 0 0 5423 8426 19 101 100 100 100 100 35933 39523 .558 1.793 1.742 1.975 1.655 3.934 52 317 1.771 .91 80 1800 6800 32 40 12 20 0 20406 140 20266 1.575 22199 22059 .635 1.53 .656 .614
2 13331 23351 67 164 13263 23187 15215 25718 74 179 15147 25554 0 0 5738 8245 23 90 100 100 100 100 36450 40701 .572 1.748 1.687 2.195 1.659 3.795 52 269 1.695 .96 80 1960 6800 32 40 28 36 0 20515 144 20371 1.536 22594 22450 .651 1.482 .619 .568
3 15919 14035 72 170 15847 13864 18927 17419 79 204 18855 17248 0 0 7195 7292 29 203 100 88 100 88 29711 36103 1.143 .875 .915 .623 .9 4.449 52 305 .901 .94 90 2100 6800 31 40 41 50 0 12330 149 12180 .769 15303 15153 1.301 .804 -.38 -.315
4 10070 14481 77 191 9992 14289 14021 22136 122 371 13944 21945 0 0 7079 12053 350 1179 75 69 73 63 24281 35889 .699 1.43 1.574 1.043 1.558 3.991 52 301 1.676 .92 90 2250 6810 32 41 56 65 0 12722 168 12554 1.256 19447 19280 .796 1.383 .329 .467
5 667 269 82 175 584 94 733 240 101 210 650 65 0 0 201 121 77 180 100 19 96 1 678 715 6.213 .161 .1 .148 .153 4.474 52 263 .153 .36 80 2410 6800 32 40 73 81 0 236 154 83 .141 211 57 7.072 .088 -2.822 -3.509
6 7430 8843 117 213 7313 8630 7312 8760 141 233 7195 8547 0 0 1164 1992 78 126 100 100 100 100 15943 15742 .847 1.18 1.188 1.156 1.188 1.907 52 255 1.262 .91 90 2560 6820 33 42 87 96 0 7769 187 7582 1.037 7696 7509 .965 1.044 .052 .062
7 206 170 86 180 119 -10 208 144 97 214 121 -36 0 0 51 92 48 151 90 3 73 1 109 85 null null null .544 .671 5.483 52 306 -1 -1 90 2710 6800 31 40 102 111 -50 149 158 -9 null 127 -32 null null null null
8 16299 13548 78 176 16220 13372 20254 18008 84 198 20176 17831 0 0 7989 8002 31 140 98 90 98 86 29592 38007 1.213 .824 .884 .659 .874 3.756 52 295 .884 .96 90 2860 6800 31 40 117 126 -100 11903 155 11748 .724 15821 15665 1.381 .776 -.465 -.365
9 111 151 72 179 39 -27 110 135 82 209 38 -43 0 0 26 73 36 144 53 1 13 0 12 -5 null null null 1.429 1.556 4.796 52 309 29.685 .07 90 3010 6790 30 39 132 141 -50 133 157 -24 null 119 -38 null null null null
10 159 426 73 171 86 254 143 320 86 215 70 149 0 0 155 670 60 205 59 32 1 5 340 219 .339 2.953 2.129 2.103 2.224 3.633 52 309 4.328 .76 90 3160 6790 30 39 147 156 0 374 150 223 2.595 281 131 .385 1.87 1.376 .903
11 500 787 77 186 422 600 540 819 91 250 463 633 0 0 213 307 58 315 92 82 90 50 1022 1096 .703 1.422 1.367 1.467 1.43 3.387 52 308 2.596 .56 90 3310 6790 30 39 162 171 0 691 163 527 1.249 720 556 .801 1.201 .321 .264
12 283 865 74 198 208 666 295 995 79 221 220 797 0 0 115 445 29 132 90 78 86 71 874 1017 .312 3.202 3.623 2.554 3.086 4.024 52 309 4.142 .86 90 3460 6790 30 39 177 186 0 760 174 585 2.813 874 700 .355 3.183 1.492 1.67
13 274 401 70 167 203 233 279 404 75 188 208 236 0 0 89 125 23 104 96 84 92 59 436 444 .871 1.148 1.135 1.117 1.062 3.36 52 241 2.216 .44 80 3620 6800 32 40 194 202 0 352 147 205 1.008 355 207 .992 .997 .012 -.005
14 158 226 74 173 84 53 162 208 79 204 88 35 0 0 47 161 31 132 86 13 65 1 137 123 1.585 .631 .398 .74 .834 5.963 52 280 18.282 .08 90 3760 6790 30 39 207 216 -50 199 152 47 .554 183 31 1.804 .349 -.851 -1.517
15 70 178 70 184 0 -6 57 89 76 209 -13 -95 0 0 41 357 25 140 9 9 5 3 -6 -108 null null null 6.1 5.658 3.483 52 311 34.877 .26 90 3910 6790 30 39 222 231 -50 156 162 -5 null 78 -83 null null null null
16 1592 1307 71 188 1521 1119 1730 1369 77 213 1659 1181 0 0 476 456 27 120 100 94 100 92 2640 2840 1.359 .736 .712 .655 .723 3.021 52 312 .743 .93 90 4060 6790 30 39 237 246 0 1148 165 983 .646 1203 1038 1.547 .625 -.63 -.677
17 86 194 71 186 15 7 87 169 77 224 15 -17 0 0 23 110 26 155 19 7 1 3 22 -2 2.143 .467 null 3.797 3.438 7.449 52 291 28.568 .29 90 4210 6790 30 39 252 261 -50 170 163 6 .41 148 -15 2.439 null -1.286 null
18 63 102 70 191 -7 -89 56 72 85 272 -14 -119 0 0 21 96 86 486 0 0 0 0 -96 -133 null null null 8.15 7.445 4.957 52 309 12.402 .38 90 4360 6790 30 39 267 276 -50 90 168 -78 null 63 -105 null null null null
19 460 305 70 173 389 132 445 290 82 229 374 117 0 0 102 112 69 371 100 3 100 0 521 491 2.947 .339 .313 .26 .339 4.29 52 255 .825 .43 80 4530 6790 31 39 285 293 0 268 152 116 .298 255 103 3.354 .275 -1.746 -1.863
20 1801 4973 70 184 1730 4789 1964 5052 80 226 1893 4868 0 0 496 1010 39 220 100 100 100 100 6519 6761 .361 2.768 2.572 2.927 2.65 2.311 52 217 2.75 .96 80 4670 6800 32 40 299 307 0 4369 162 4207 2.432 4438 4277 .411 2.259 1.282 1.176

Total number of rows: 44544

Table truncated, full table size 9687 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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