NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989684 Query DataSets for GSM989684
Status Public on Aug 23, 2012
Title PC 37T
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 37
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 72
pre-operation treatment: None
individual: PC 188T
disease free survival: 69.50
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/2008-11/81782.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
1 625 447 37 103 587 343 617 399 42 117 579 296 0 0 135 173 18 78 100 98 100 92 930 875 1.711 .584 .511 .528 .512 3.277 52 363 .569 .79 90 1540 7790 34 43 33 42 0 474 109 364 .619 423 314 1.615 .542 -.691 -.884
2 796 587 38 100 758 486 800 581 44 118 761 480 0 0 193 206 25 82 100 98 100 96 1244 1241 1.56 .641 .631 .587 .688 3.335 52 294 .638 .88 90 1700 7790 34 43 49 58 0 622 106 515 .68 616 509 1.472 .668 -.557 -.581
3 523 908 40 106 483 802 509 892 44 123 469 785 0 0 113 218 22 82 100 100 100 100 1285 1254 .602 1.66 1.674 1.639 1.705 2.678 52 307 1.682 .9 90 1840 7790 34 43 63 72 0 962 112 850 1.76 945 832 .568 1.774 .815 .827
4 1315 904 42 113 1272 791 1301 913 47 139 1258 799 0 0 408 293 24 144 100 98 100 96 2063 2057 1.608 .622 .635 .605 .613 2.747 52 263 .589 .93 90 1990 7790 34 43 78 87 0 958 120 838 .659 968 847 1.517 .673 -.601 -.571
5 59 78 40 102 19 -23 55 71 42 121 15 -30 0 0 21 43 12 71 53 2 30 1 -4 -15 null null null 2.104 3.074 13.966 80 293 37.506 .06 100 2140 7790 34 44 93 103 -50 83 108 -24 null 75 -32 null null null null
6 239 415 43 104 195 310 241 426 46 130 198 321 0 0 48 138 13 88 100 92 100 82 505 519 .629 1.59 1.621 1.423 1.697 3.621 52 269 1.779 .75 90 2300 7790 34 43 109 118 0 440 110 329 1.685 451 340 .594 1.718 .753 .781
7 52 142 44 123 8 19 50 110 48 137 5 -12 0 0 25 76 17 85 28 18 6 3 27 -7 .421 2.375 null 4.084 4.06 6.683 32 221 18.672 .18 70 2460 7750 31 38 126 133 0 150 130 20 2.517 117 -13 .397 null 1.332 null
8 721 1329 42 125 679 1203 750 1336 45 157 708 1210 0 0 170 254 14 176 100 100 100 100 1882 1918 .564 1.772 1.709 1.811 1.788 2.598 52 262 1.651 .93 90 2600 7780 33 42 139 148 0 1409 132 1275 1.878 1416 1282 .533 1.811 .909 .857
9 55 110 42 135 12 -25 49 85 46 170 7 -50 0 0 22 81 16 199 27 1 12 0 -13 -43 null null null 7.937 9.006 10.568 80 289 53.723 .16 100 2750 7770 32 42 154 164 -50 117 143 -26 null 90 -53 null null null null
10 50 86 42 125 8 -39 49 78 45 148 7 -47 0 0 12 47 14 131 28 0 7 0 -31 -40 null null null 8.639 11.552 8.854 80 273 45.676 .16 100 2900 7770 32 42 169 179 -50 91 132 -41 null 83 -50 null null null null
11 67 130 42 131 25 -1 65 120 43 145 23 -11 0 0 20 81 11 76 71 11 51 2 24 12 null null null 1.204 1.363 8.906 80 273 31.471 .09 100 3050 7770 32 42 184 194 -50 138 139 -1 null 127 -12 null null null null
12 61 104 42 134 18 -29 57 89 45 148 15 -44 0 0 22 61 12 81 55 5 27 1 -11 -29 null null null 3.861 3.732 12.86 80 336 49.822 .08 100 3200 7770 32 42 199 209 -50 110 142 -31 null 94 -47 null null null null
13 70 132 48 114 21 18 57 88 50 141 9 -26 0 0 30 111 14 121 33 25 25 0 39 -17 1.167 .857 null 10.223 8.774 8.472 12 68 18.993 .18 40 3370 7750 33 37 219 223 0 140 121 19 .908 93 -28 1.101 null -.139 null
14 55 110 44 138 10 -27 52 93 47 166 7 -44 0 0 18 76 14 132 35 3 8 1 -17 -37 null null null 6.247 6.299 6.504 80 320 21.294 .36 100 3510 7770 32 42 230 240 -50 117 146 -29 null 99 -47 null null null null
15 47 95 42 128 5 -33 47 82 45 155 5 -46 0 0 9 68 12 111 17 3 0 2 -28 -41 null null null 7.64 8.658 6.958 80 321 167.596 .04 100 3660 7770 32 42 245 255 -50 101 136 -35 null 87 -49 null null null null
16 87 163 45 123 42 40 87 152 47 137 42 29 0 0 24 54 15 62 83 16 58 8 82 71 1.05 .952 .69 1.443 .883 11.025 12 101 6.719 .21 50 3810 7790 36 41 262 267 0 173 130 42 1.009 161 31 .991 .732 .013 -.45
17 47 88 42 144 5 -55 47 81 44 156 5 -62 0 0 9 48 12 83 17 2 2 1 -50 -57 null null null 11.539 12.175 6.692 80 310 91.045 .07 100 3960 7770 32 42 275 285 -50 93 153 -58 null 86 -66 null null null null
18 42 69 42 139 0 -69 42 57 44 151 0 -82 0 0 8 40 11 82 11 0 0 0 -69 -82 null null null 13.522 13.033 4.552 80 274 6.347 .78 100 4110 7760 31 41 290 300 -50 73 147 -73 null 60 -87 null null null null
19 51 83 42 127 9 -43 51 74 44 144 9 -53 0 0 12 41 12 79 31 0 12 0 -34 -44 null null null 9.566 8.113 6.191 80 338 76.949 .06 100 4260 7760 31 41 305 315 -50 88 135 -46 null 78 -56 null null null null
20 172 662 40 120 132 542 177 638 41 134 137 518 0 0 38 212 10 64 100 98 100 98 674 655 .244 4.106 3.781 3.868 3.967 3.546 52 279 4.665 .85 90 4410 7770 32 41 320 329 0 702 127 574 4.352 676 549 .23 4.007 2.122 2.003

Total number of rows: 44544

Table truncated, full table size 9355 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap