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Sample GSM989777 Query DataSets for GSM989777
Status Public on Aug 23, 2012
Title PC 370T
Sample type RNA
 
Channel 1
Source name Human 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 370T
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 63
pre-operation treatment: None
individual: PC 184T
disease free survival: 44.60
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/2008-08/80897.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 14953 8968 148 129 14805 8839 20494 12711 160 160 20346 12582 0 0 11277 6881 74 141 82 78 80 78 23644 32928 1.675 .597 .618 .681 .62 2.386 52 366 .602 .95 90 2090 7260 49 58 36 45 0 9724 140 9584 .647 13783 13643 1.545 .671 -.627 -.577
2 14268 9163 154 137 14114 9026 16612 10787 168 176 16458 10650 0 0 6466 4568 73 162 100 96 100 94 23140 27108 1.564 .64 .647 .542 .642 2.595 52 242 .644 .97 80 2250 7270 51 59 53 61 0 9936 149 9787 .693 11697 11548 1.442 .702 -.528 -.511
3 22645 29409 164 142 22481 29267 26558 32505 185 185 26394 32363 0 0 8874 9755 95 179 100 100 100 100 51748 58757 .768 1.302 1.226 1.383 1.253 1.579 52 238 1.276 .96 80 2400 7280 52 60 68 76 0 31889 154 31735 1.412 35246 35092 .708 1.33 .497 .411
4 15365 10826 152 121 15213 10705 16524 10444 168 154 16372 10323 0 0 5163 2964 78 139 100 100 100 100 25918 26695 1.421 .704 .631 .749 .676 1.534 52 245 .662 .95 80 2550 7280 52 60 83 91 0 11739 131 11608 .763 11325 11193 1.311 .684 -.39 -.549
5 716 251 179 147 537 104 724 214 206 202 545 67 0 0 230 120 112 251 98 15 90 0 641 612 5.163 .194 .123 .214 .228 2.803 52 245 .858 .19 80 2710 7270 51 59 99 107 0 272 159 113 .21 232 73 4.762 .133 -2.252 -2.907
6 7564 12498 230 170 7334 12328 7317 12438 274 240 7087 12268 0 0 1248 3547 167 479 100 100 100 100 19662 19355 .595 1.681 1.731 1.609 1.701 1.366 52 287 1.845 .95 90 2860 7270 50 59 113 122 0 13552 184 13368 1.823 13487 13302 .549 1.877 .866 .908
7 296 209 157 148 139 61 292 189 180 167 135 41 0 0 105 130 90 105 67 28 26 9 200 176 2.279 .439 .304 .644 .876 4.21 52 304 2.025 .24 90 3010 7270 50 59 128 137 -50 227 160 66 .476 205 44 2.101 .329 -1.071 -1.602
8 21609 25725 149 137 21460 25588 26020 29666 164 173 25871 29529 0 0 10138 10335 74 178 100 100 98 100 47048 55400 .839 1.192 1.141 1.463 1.193 2.276 52 251 1.158 .95 80 3160 7280 52 60 144 152 0 27894 149 27746 1.293 32167 32019 .773 1.238 .371 .308
9 255 284 151 121 104 163 236 255 181 189 85 134 0 0 93 146 182 282 18 21 0 0 267 219 .638 1.567 1.576 1.538 1.832 4.815 32 169 1.488 .84 60 3310 7270 52 58 160 166 0 308 131 177 1.699 277 145 .588 1.709 .765 .773
10 229 166 148 140 81 26 221 157 179 210 73 17 0 0 82 75 161 455 13 0 0 0 107 90 3.115 .321 .233 .685 .952 3.025 52 296 6.102 .13 90 3460 7270 50 59 173 182 -50 180 152 28 .348 170 18 2.873 .253 -1.523 -1.986
11 944 1238 142 150 802 1088 927 1231 156 210 785 1081 0 0 246 378 68 496 100 93 100 56 1890 1866 .737 1.357 1.377 1.337 1.327 1.452 32 209 1.446 .88 70 3610 7270 51 58 189 196 0 1342 163 1180 1.471 1335 1172 .68 1.493 .557 .578
12 476 3875 135 133 341 3742 484 3776 148 164 349 3643 0 0 168 1070 59 153 96 100 88 100 4083 3992 .091 10.974 10.438 11.939 10.813 1.673 52 289 11.745 .83 90 3760 7280 51 60 203 212 0 4202 144 4058 11.899 4094 3950 .084 11.319 3.573 3.501
13 477 295 136 138 341 157 492 276 151 156 356 138 0 0 137 161 62 112 100 53 93 34 498 494 2.172 .46 .388 .417 .501 3.582 32 209 .826 .4 70 3910 7270 51 58 219 226 0 320 150 170 .499 299 150 2.003 .42 -1.002 -1.25
14 275 268 149 142 126 126 273 229 177 192 124 87 0 0 74 121 131 191 43 31 6 3 252 211 1 1 .702 1.17 1.085 2.815 32 169 3.42 .56 60 4060 7270 52 58 235 241 0 291 154 137 1.084 248 94 .922 .761 .117 -.394
15 194 138 147 142 47 -4 190 133 172 181 43 -9 0 0 78 90 126 165 13 5 1 0 43 34 null null null 1.104 1.376 5.17 52 307 1.945 .52 90 4210 7270 50 59 248 257 -50 150 154 -4 null 144 -10 null null null null
16 1229 467 143 141 1086 326 1306 472 159 190 1163 331 0 0 343 218 93 259 100 59 98 25 1412 1494 3.331 .3 .285 .256 .313 2.539 52 234 .39 .48 80 4370 7270 51 59 265 273 0 506 153 353 .325 512 359 3.072 .309 -1.619 -1.696
17 221 158 141 121 80 37 219 138 159 172 78 17 0 0 63 98 99 243 40 1 0 0 117 95 2.162 .463 .218 1.378 1.228 6.26 52 260 8.751 .09 90 4510 7270 50 59 278 287 -50 171 131 40 .501 150 18 1.994 .236 -.996 -2.081
18 173 123 160 139 13 -16 166 114 179 193 6 -25 0 0 50 72 106 244 5 1 0 0 -3 -19 null null null 1.144 1.039 4.297 52 294 3.023 .42 90 4660 7270 50 59 293 302 -50 133 151 -17 null 124 -27 null null null null
19 359 339 154 136 205 203 364 305 164 165 210 169 0 0 157 201 71 140 76 57 71 28 408 379 1.01 .99 .805 .778 .861 3.128 52 311 1.525 .6 90 4810 7270 50 59 308 317 -50 368 147 220 1.074 331 183 .931 .873 .103 -.197
20 2101 4162 150 141 1951 4021 2619 5591 162 170 2469 5450 0 0 1326 2834 67 129 82 78 80 75 5972 7919 .485 2.061 2.207 1.622 2.004 2.163 52 294 2.221 .96 90 4960 7270 50 59 323 332 0 4513 153 4360 2.235 6062 5910 .447 2.394 1.16 1.259

Total number of rows: 44544

Table truncated, full table size 9655 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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