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Sample GSM989703 Query DataSets for GSM989703
Status Public on Aug 23, 2012
Title PC 627N
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 627N2
Organism Homo sapiens
Characteristics individual: PC 627N
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/2008-08/81099.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 7561 10687 222 173 7338 10514 8329 11883 271 227 8106 11710 0 0 2455 3005 163 158 100 100 100 100 17852 19816 .698 1.433 1.445 1.489 1.386 1.157 32 235 1.412 .98 70 1740 6720 24 31 22 29 0 10654 172 10481 1.428 11846 11674 .7 1.44 .514 .526
2 8104 10741 304 263 7799 10477 9570 12826 378 327 9266 12562 0 0 3722 4480 245 228 96 100 96 100 18276 21828 .744 1.343 1.356 1.522 1.349 1.483 32 174 1.324 .98 60 1890 6720 25 31 38 44 0 10708 262 10444 1.339 12786 12523 .747 1.351 .421 .435
3 11366 12768 367 303 10999 12465 13997 16045 486 394 13630 15741 0 0 4778 6019 325 270 100 100 100 100 23464 29371 .882 1.133 1.155 1.049 1.123 1.164 32 228 1.171 .98 70 2030 6720 24 31 51 58 0 12728 302 12426 1.13 15995 15692 .885 1.151 .176 .203
4 8866 12388 294 253 8571 12134 11226 15689 373 328 10932 15435 0 0 4870 6556 258 227 92 98 90 98 20705 26367 .706 1.416 1.412 1.509 1.425 1.384 52 312 1.407 .99 80 2190 6720 24 32 67 75 0 12349 252 12096 1.411 15640 15387 .709 1.408 .497 .493
5 1155 275 271 206 884 68 1167 236 287 236 896 29 0 0 229 103 120 118 100 25 100 8 952 925 13 .077 .032 .052 .066 3.498 12 102 .108 .35 50 2340 6730 26 31 83 88 0 274 205 68 .077 235 29 13.041 .032 -3.705 -4.954
6 6436 8320 286 281 6150 8039 7550 9300 302 319 7263 9019 0 0 2896 2914 123 173 96 100 92 100 14189 16282 .765 1.307 1.242 1.725 1.353 1.885 52 245 1.242 .97 80 2490 6720 24 32 97 105 0 8294 280 8014 1.303 9271 8991 .767 1.238 .382 .308
7 347 281 310 315 36 -34 321 240 374 374 11 -75 0 0 129 167 218 231 7 5 3 0 2 -64 null null null 2.055 2.453 3.581 52 270 1.386 .66 90 2630 6710 22 31 110 119 -50 280 314 -34 null 239 -75 null null null null
8 9549 11153 332 311 9216 10842 8211 13689 402 370 7878 13378 0 0 7368 8042 232 258 96 100 94 96 20058 21256 .85 1.176 1.698 1.268 1.169 1.274 52 319 1.134 .99 90 2780 6710 22 31 125 134 0 11118 310 10808 1.173 13646 13336 .853 1.693 .23 .759
9 230 199 229 187 1 11 233 195 294 248 4 8 0 0 76 91 191 209 1 3 0 0 12 12 .091 11 2 1.278 1.329 3.397 52 313 1.133 .7 90 2940 6710 22 31 141 150 -50 198 186 11 10.966 194 8 .091 1.994 3.455 .996
10 212 193 165 127 47 65 201 185 184 150 36 57 0 0 77 88 102 120 17 21 3 3 112 93 .723 1.383 1.583 1.189 1.141 4.185 52 292 3.188 .37 90 3090 6710 22 31 156 165 -50 192 127 65 1.379 184 57 .725 1.578 .463 .658
11 445 523 165 109 280 413 449 518 180 126 284 409 0 0 148 168 79 69 96 100 78 96 693 693 .678 1.475 1.44 1.738 1.439 2.724 32 176 1.556 .71 60 3250 6710 24 30 174 180 0 521 109 412 1.47 516 408 .68 1.436 .556 .522
12 387 2670 164 125 222 2544 374 2678 179 139 210 2553 0 0 122 808 93 101 87 100 59 100 2766 2763 .087 11.459 12.157 11.846 11.818 1.44 32 210 13.372 .7 70 3390 6720 24 31 187 194 0 2662 125 2536 11.424 2670 2545 .088 12.119 3.514 3.599
13 353 242 165 115 188 126 363 224 181 132 198 109 0 0 97 93 73 77 90 68 68 31 314 307 1.492 .67 .551 .627 .712 2.194 32 214 .961 .5 70 3550 6710 23 30 203 210 0 241 115 126 .668 223 109 1.497 .549 -.582 -.866
14 385 352 157 104 228 248 379 329 169 116 221 224 0 0 77 89 60 68 91 100 91 91 476 445 .919 1.088 1.014 1.109 1.045 1.621 12 104 1.163 .68 50 3690 6710 24 29 218 223 0 351 104 247 1.084 328 223 .922 1.01 .117 .015
15 198 81 169 109 28 -28 191 80 183 121 22 -29 0 0 59 51 76 68 23 1 0 1 0 -7 null null null 2.482 2.112 2.978 52 314 2.69 .14 90 3840 6710 22 31 231 240 -50 81 109 -28 null 80 -29 null null null null
16 2177 1361 179 110 1997 1250 2151 1333 187 123 1971 1222 0 0 301 315 71 71 100 100 100 100 3247 3193 1.598 .626 .62 .612 .591 1.062 32 202 .641 .95 70 4000 6710 23 30 248 255 0 1357 110 1246 .624 1329 1218 1.603 .618 -.68 -.694
17 233 148 157 103 76 45 212 140 175 115 55 37 0 0 91 66 72 66 44 34 17 9 121 92 1.689 .592 .673 .982 1.069 3.476 52 295 1.281 .23 90 4140 6700 21 30 261 270 -50 148 103 45 .59 140 37 1.694 .671 -.761 -.576
18 184 77 149 101 34 -23 183 68 160 116 33 -32 0 0 65 45 62 72 30 3 11 1 11 1 null null null .903 1.165 3.839 52 301 2.183 .21 90 4290 6700 21 30 276 285 -50 77 101 -23 null 68 -32 null null null null
19 352 243 152 111 200 131 355 211 165 124 202 99 0 0 131 110 66 75 84 67 65 30 331 301 1.527 .655 .49 .59 .695 2.24 52 288 .799 .56 80 4450 6700 22 30 293 301 0 242 111 131 .653 210 99 1.531 .489 -.615 -1.033
20 1619 5155 145 104 1474 5051 1621 5338 157 119 1476 5233 0 0 487 1110 61 71 100 100 100 100 6525 6709 .292 3.427 3.545 3.566 3.569 1.072 32 215 3.429 .96 70 4600 6710 23 30 308 315 0 5139 104 5035 3.416 5321 5217 .293 3.534 1.772 1.821

Total number of rows: 44544

Table truncated, full table size 9821 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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