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Sample GSM989798 Query DataSets for GSM989798
Status Public on Aug 23, 2012
Title PC 83T
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 PT 83
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 56
pre-operation treatment: None
individual: PC 601T
disease free survival: 0.03
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/2008-11/81785.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 GPL15972
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 5920 4703 35 102 5885 4600 6252 5200 40 115 6217 5097 0 0 1433 1778 31 69 100 100 100 100 10485 11314 1.279 .782 .82 .716 .824 3.545 52 364 .785 .94 90 1600 7360 31 40 39 48 0 3827 83 3743 .636 4231 4147 1.572 .667 -.653 -.584
2 4928 4014 34 100 4893 3913 5412 4662 37 119 5377 4561 0 0 1558 1641 11 82 100 100 100 100 8806 9938 1.25 .8 .848 .765 .822 4.478 52 285 .787 .92 90 1750 7360 31 40 54 63 0 3266 81 3184 .651 3793 3711 1.537 .69 -.62 -.535
3 1989 3539 36 116 1952 3423 2628 3900 40 157 2592 3783 0 0 1251 2585 15 135 95 85 92 80 5375 6375 .57 1.754 1.459 1.601 1.807 8.275 80 356 1.854 .94 100 1900 7360 31 41 69 79 0 2879 94 2785 1.427 3173 3078 .701 1.188 .513 .248
4 5121 4103 37 113 5084 3989 5614 4776 40 126 5576 4662 0 0 1774 2025 14 69 100 94 100 90 9073 10238 1.275 .785 .836 .558 .814 6.125 52 285 .806 .94 90 2050 7350 30 39 84 93 0 3338 92 3246 .638 3886 3793 1.566 .68 -.647 -.556
5 121 170 36 96 84 73 116 142 39 105 79 46 0 0 50 154 10 56 96 42 94 21 157 125 1.151 .869 .582 .821 .808 6.195 52 278 2.233 .22 90 2210 7350 30 39 100 109 0 138 78 59 .707 116 37 1.414 .474 -.5 -1.078
6 1022 1334 42 99 980 1235 1043 1426 47 121 1001 1327 0 0 226 426 20 98 100 98 100 98 2215 2328 .794 1.26 1.326 1.174 1.322 3.623 52 289 1.246 .92 90 2350 7350 30 39 114 123 0 1085 81 1005 1.025 1160 1080 .975 1.079 .036 .109
7 75 139 42 108 33 31 77 141 46 116 35 33 0 0 24 69 15 60 71 21 56 6 64 68 1.065 .939 .943 1.971 1.632 6.629 32 157 5.749 .1 60 2480 7350 32 38 129 135 0 113 88 25 .764 115 27 1.308 .767 -.388 -.382
8 2439 4401 36 100 2402 4300 2567 4852 44 142 2530 4752 0 0 561 1849 48 278 100 92 100 92 6702 7282 .559 1.79 1.878 1.364 1.851 5.742 52 275 1.9 .94 80 2660 7350 31 39 146 154 0 3581 81 3499 1.457 3948 3866 .687 1.528 .543 .612
9 54 100 35 109 18 -8 53 90 43 141 18 -18 0 0 17 46 45 250 6 0 0 0 10 0 null null null 3.423 2.91 10.184 80 332 12.355 .28 100 2810 7340 29 39 160 170 -50 81 89 -7 null 73 -15 null null null null
10 56 122 34 105 22 17 53 98 38 125 18 -7 0 0 23 93 18 90 47 13 22 2 39 11 1.294 .773 null 2.385 2.187 6.837 80 331 7.217 .47 110 2960 7340 28 39 174 185 0 99 85 14 .629 80 -6 1.591 null -.669 null
11 196 269 35 103 160 165 192 266 37 129 157 162 0 0 42 109 11 113 100 61 100 28 325 319 .97 1.031 1.032 .884 1.116 5.374 52 237 1.871 .41 80 3110 7350 31 39 191 199 0 219 84 134 .839 216 132 1.192 .84 -.253 -.252
12 137 270 33 116 103 154 136 223 37 141 102 106 0 0 21 139 11 123 100 43 100 28 257 208 .669 1.495 1.039 1.123 1.22 5.635 32 203 3.189 .51 70 3260 7350 31 38 206 213 0 220 94 125 1.217 181 86 .822 .846 .283 -.242
13 142 159 33 103 108 56 112 134 36 112 78 30 0 0 126 119 9 56 100 28 100 9 164 108 1.929 .519 .385 .395 .497 7.209 32 200 .796 .74 70 3410 7360 32 39 221 228 0 129 84 46 .422 109 24 2.37 .313 -1.245 -1.676
14 66 105 40 108 25 -2 66 122 45 122 25 14 0 0 20 47 16 70 58 0 41 0 23 39 null null .56 1.549 .918 7.465 12 103 7.311 .18 50 3540 7340 31 36 235 240 0 85 88 -2 null 99 11 null .456 null -1.134
15 111 492 35 103 76 389 38 93 41 122 2 -10 0 0 546 2525 29 102 2 10 2 6 465 -8 .195 5.118 null 4.371 7.99 16.705 80 381 -1 -1 100 3700 7340 29 39 249 259 -50 400 84 317 4.165 76 -8 .24 null 2.058 null
16 179 435 34 89 145 345 172 412 37 98 138 322 0 0 28 129 18 49 100 100 100 100 490 460 .42 2.379 2.333 2.254 2.433 3.284 32 179 2.976 .82 70 3870 7350 31 38 267 274 0 354 72 281 1.936 335 262 .517 1.899 .953 .925
17 45 103 33 95 11 8 45 96 37 110 11 1 0 0 12 41 16 67 36 11 3 0 19 12 1.375 .727 .091 3.822 4.155 8.34 80 304 64.467 .05 100 4010 7340 29 39 280 290 -50 84 77 7 .592 78 1 1.69 .074 -.757 -3.757
18 38 100 34 100 3 0 36 89 37 113 2 -11 0 0 8 56 12 66 13 12 1 2 3 -9 null null null 6.399 7.79 8.222 80 338 12.987 .35 100 4160 7340 29 39 295 305 -50 81 81 0 null 72 -9 null null null null
19 92 152 34 103 57 49 88 135 38 121 54 31 0 0 20 85 12 67 100 28 100 9 106 85 1.163 .86 .574 .817 .816 7.352 32 227 6.173 .15 70 4320 7340 30 37 312 319 0 124 84 40 .699 110 25 1.43 .467 -.516 -1.098
20 671 2463 36 99 635 2363 706 2597 38 122 670 2497 0 0 147 730 10 103 100 100 100 100 2998 3167 .269 3.721 3.727 3.571 3.875 3.38 52 275 3.947 .91 90 4480 7350 30 39 327 336 0 2004 81 1923 3.028 2113 2032 .33 3.032 1.598 1.6

Total number of rows: 44544

Table truncated, full table size 8923 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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