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Sample GSM989782 Query DataSets for GSM989782
Status Public on Aug 23, 2012
Title PC 646N
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 646N2
Organism Homo sapiens
Characteristics individual: PC 646N
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/2008-08/81138.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) [email protected]
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 3536 5482 90 109 3446 5372 3965 5718 96 124 3875 5608 0 0 1265 1700 35 88 100 100 100 100 8818 9483 .641 1.559 1.447 1.623 1.631 3.462 52 285 1.528 .86 80 2030 7170 21 29 43 51 0 4419 88 4330 1.257 4609 4521 .796 1.167 .33 .222
2 2909 4783 93 121 2816 4662 3560 5259 107 149 3467 5138 0 0 1305 2199 73 156 96 94 96 92 7478 8605 .604 1.656 1.482 1.538 1.725 5.507 52 258 1.681 .86 80 2180 7160 20 28 58 66 0 3856 98 3758 1.335 4239 4142 .749 1.195 .416 .257
3 5028 6153 92 112 4936 6040 5706 7303 101 130 5613 7191 0 0 1990 3592 39 81 100 94 100 86 10976 12804 .817 1.224 1.281 .842 1.271 4.889 52 279 1.358 .87 80 2330 7150 19 27 73 81 0 4960 90 4869 .986 5887 5797 1.014 1.033 -.02 .046
4 3100 4570 94 107 3006 4462 3972 5435 105 174 3877 5327 0 0 1896 3939 46 332 90 67 86 63 7468 9204 .674 1.484 1.374 .957 1.629 5.788 52 318 1.9 .87 90 2480 7150 18 27 87 96 0 3684 86 3597 1.197 4381 4294 .836 1.108 .259 .147
5 196 149 93 121 102 28 187 123 106 166 93 2 0 0 83 100 62 221 63 7 36 0 130 95 3.643 .275 .022 .748 .652 8.57 52 285 -1 -1 90 2630 7150 18 27 102 111 -50 120 98 23 .221 99 2 4.519 .017 -2.176 -5.85
6 1419 3706 108 140 1310 3565 1622 4151 127 179 1513 4010 0 0 692 1935 101 149 92 92 88 91 4875 5523 .367 2.721 2.65 2.796 2.762 6.734 80 315 2.908 .9 100 2780 7160 19 29 117 127 0 2987 113 2874 2.194 3346 3233 .456 2.137 1.133 1.095
7 177 133 98 135 78 -2 119 100 106 159 21 -35 0 0 243 112 41 111 40 17 23 3 76 -14 null null null 4.666 4.582 8.654 52 260 -1 -1 90 2930 7160 19 28 132 141 -50 107 109 -2 null 81 -28 null null null null
8 4782 6430 92 138 4689 6291 5608 7630 98 154 5516 7491 0 0 2125 3249 38 92 100 94 98 94 10980 13007 .745 1.342 1.358 1.14 1.325 5.822 52 236 1.392 .88 80 3080 7160 20 28 148 156 0 5183 111 5071 1.082 6151 6039 .925 1.095 .113 .131
9 109 123 85 112 23 11 98 116 90 129 12 3 0 0 46 58 33 97 40 7 17 0 34 15 2.091 .478 .25 1.574 1.638 5.802 52 291 16.899 .04 90 3230 7150 18 27 162 171 -50 99 90 9 .386 94 2 2.594 .202 -1.375 -2.311
10 114 161 90 121 23 40 106 148 102 184 15 27 0 0 40 95 83 504 9 0 0 0 63 42 .575 1.739 1.8 2.673 2.519 5.278 52 301 -1 -1 90 3380 7150 18 27 177 186 -50 130 98 32 1.402 119 22 .713 1.451 .487 .537
11 231 416 95 147 135 269 214 418 107 207 118 271 0 0 90 163 90 548 63 1 28 0 404 389 .502 1.993 2.297 2.459 1.962 4.249 52 245 32.291 .18 80 3540 7160 20 28 194 202 0 335 118 217 1.606 337 218 .623 1.851 .684 .889
12 171 1672 98 128 72 1543 178 1707 101 154 80 1579 0 0 50 418 37 130 76 100 51 100 1615 1659 .047 21.431 19.738 20.82 17.906 2.844 52 236 24.015 .54 80 3690 7160 20 28 209 217 0 1348 103 1244 17.276 1376 1273 .058 15.911 4.111 3.992
13 164 152 103 148 60 3 153 130 110 189 50 -17 0 0 64 85 46 184 53 1 26 0 63 33 20 .05 null 1.279 1.302 6.865 52 291 52.772 .03 90 3840 7150 18 27 223 232 -50 123 119 2 .04 105 -14 24.81 null -4.633 null
14 131 163 98 139 33 23 127 139 105 175 29 0 0 0 44 87 42 135 38 11 11 0 56 29 1.435 .697 null 1.721 1.746 5.823 52 291 18.664 .09 90 3990 7150 18 27 238 247 -50 131 112 19 .562 112 0 1.78 null -.832 null
15 112 81 91 112 21 -30 117 67 96 130 25 -44 0 0 37 59 34 86 36 5 11 0 -9 -19 null null null 1.69 1.485 3.409 52 291 -10.512 -.1 90 4140 7150 18 27 253 262 -50 65 90 -24 null 54 -35 null null null null
16 460 339 95 143 364 196 447 350 101 164 351 207 0 0 154 143 37 105 98 67 94 48 560 558 1.857 .538 .59 .432 .576 5.603 52 258 .478 .53 80 4290 7150 19 27 269 277 0 273 115 158 .434 282 167 2.304 .475 -1.204 -1.073
17 118 134 93 126 25 8 111 121 100 149 18 -4 0 0 40 86 39 102 34 13 5 1 33 14 3.125 .32 null 2.895 3.666 9.621 52 291 23.997 .05 90 4440 7150 18 27 283 292 -50 108 102 6 .258 98 -3 3.877 null -1.955 null
18 119 122 92 130 27 -8 104 90 97 150 12 -40 0 0 52 103 40 103 30 11 15 7 19 -28 null null null 2.798 2.036 8.543 52 304 38.911 .03 90 4590 7150 18 27 298 307 -50 98 105 -6 null 73 -32 null null null null
19 173 243 89 130 83 112 153 201 101 155 63 70 0 0 78 156 46 106 62 43 37 18 195 133 .741 1.349 1.111 2.411 1.704 8.743 32 225 4.261 .16 70 4740 7140 18 25 314 321 0 196 105 90 1.088 162 56 .919 .896 .121 -.159
20 544 1532 97 154 446 1377 678 1600 109 216 580 1445 0 0 329 1260 69 283 71 63 67 57 1823 2025 .324 3.087 2.491 2.806 3.469 3.919 52 313 4.233 .81 90 4890 7150 18 27 328 337 0 1235 124 1110 2.489 1290 1165 .402 2.008 1.315 1.006

Total number of rows: 44544

Table truncated, full table size 9656 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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