NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989724 Query DataSets for GSM989724
Status Public on Aug 23, 2012
Title PC 527N
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 527N2
Organism Homo sapiens
Characteristics individual: PC 527N
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/2008-08/81171.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 GPL9497
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 14015 19165 62 97 13953 19067 17801 23836 66 120 17738 23738 0 0 6636 8316 25 98 100 100 100 100 33020 41476 .732 1.367 1.338 1.628 1.386 3.115 52 298 1.336 .97 80 1810 7290 21 29 49 57 0 17118 87 17030 1.221 21290 21202 .819 1.195 .288 .257
2 13572 17807 63 97 13508 17709 17963 23077 67 110 17899 22979 0 0 7952 10210 18 65 100 100 100 100 31217 40878 .763 1.311 1.284 1.308 1.34 2.821 52 261 1.297 .98 80 1960 7290 21 29 64 72 0 15905 87 15817 1.171 20612 20524 .854 1.147 .228 .197
3 14217 13267 71 106 14145 13161 14974 13695 72 118 14902 13589 0 0 2462 2136 20 63 100 100 100 100 27306 28491 1.075 .93 .912 .933 .922 1.672 32 221 .905 .97 70 2100 7290 21 28 78 85 0 11850 95 11755 .831 12232 12137 1.203 .814 -.267 -.296
4 15421 21126 67 103 15354 21023 21234 26914 70 117 21167 26810 0 0 9014 11026 21 63 100 100 100 100 36377 47977 .73 1.369 1.267 1.583 1.349 3.37 52 293 1.32 .98 80 2260 7290 21 29 94 102 0 18869 92 18777 1.223 24039 23946 .818 1.131 .29 .178
5 713 308 72 114 640 194 774 265 78 135 701 150 0 0 223 191 29 101 100 75 100 30 834 851 3.299 .303 .214 .243 .233 4.016 52 286 .335 .3 80 2410 7290 21 29 109 117 0 275 102 173 .271 237 134 3.694 .191 -1.885 -2.387
6 7716 9164 79 109 7637 9055 7918 9263 83 115 7839 9153 0 0 2069 2010 26 53 100 100 100 100 16692 16992 .843 1.186 1.168 1.23 1.165 1.873 52 275 1.147 .98 80 2560 7290 21 29 124 132 0 8185 97 8088 1.059 8273 8175 .944 1.043 .083 .061
7 266 267 77 106 189 161 251 268 79 118 174 162 0 0 50 77 24 66 100 93 100 56 350 336 1.174 .852 .931 .712 .888 3.786 32 217 .796 .64 70 2710 7290 21 28 139 146 0 238 95 144 .761 239 145 1.314 .832 -.394 -.266
8 14028 13331 72 107 13956 13223 16453 14949 76 123 16380 14842 0 0 5137 4081 23 73 100 100 100 100 27179 31222 1.055 .947 .906 1.059 .945 2.461 52 265 .916 .98 80 2860 7290 21 29 154 162 0 11907 96 11810 .846 13352 13256 1.182 .809 -.241 -.305
9 214 388 67 108 146 279 217 384 71 130 149 276 0 0 46 126 19 82 100 100 100 81 425 425 .523 1.911 1.852 1.808 2.03 2.674 32 211 2.539 .73 70 3010 7280 20 27 169 176 0 347 96 249 1.707 343 247 .586 1.654 .771 .726
10 212 343 63 94 148 249 217 346 67 124 153 252 0 0 45 91 24 118 96 93 96 56 397 405 .594 1.682 1.647 1.663 1.599 2.41 32 195 1.786 .78 70 3160 7290 21 28 184 191 0 306 84 222 1.503 309 225 .665 1.471 .588 .557
11 511 956 64 91 446 864 535 946 68 103 470 855 0 0 116 246 22 57 100 100 96 100 1310 1325 .516 1.937 1.819 1.991 1.977 2.15 32 223 1.993 .92 70 3300 7280 20 27 198 205 0 854 81 772 1.73 845 764 .578 1.625 .791 .7
12 438 2843 64 101 373 2741 422 2811 67 117 358 2710 0 0 76 429 20 69 100 100 100 100 3114 3068 .136 7.349 7.57 7.407 7.207 1.825 32 230 7.611 .95 70 3460 7280 20 27 214 221 0 2539 90 2448 6.563 2511 2420 .152 6.761 2.714 2.757
13 331 314 63 88 268 226 328 308 63 101 265 220 0 0 41 94 16 54 100 100 100 87 494 485 1.186 .843 .83 .785 .781 2.267 32 225 .842 .78 70 3610 7280 20 27 229 236 0 280 79 202 .753 275 196 1.328 .741 -.409 -.431
14 150 200 58 83 92 117 150 192 61 92 91 109 0 0 48 74 16 50 88 84 86 51 209 200 .786 1.272 1.198 1.278 1.062 3.601 52 224 1.631 .56 80 3760 7290 21 29 244 252 0 179 74 105 1.136 171 97 .88 1.07 .184 .097
15 75 110 60 94 14 16 72 100 62 107 12 6 0 0 18 49 16 55 42 18 17 8 30 18 .875 1.143 .5 2.392 2.216 5.14 80 375 9.579 .24 100 3910 7280 19 29 258 268 -50 98 84 14 1.021 89 5 .98 .447 .03 -1.163
16 887 716 58 96 828 619 862 716 61 104 803 619 0 0 96 171 15 56 100 100 100 100 1447 1422 1.338 .748 .771 .726 .722 1.901 32 201 .775 .92 70 4060 7280 20 27 274 281 0 640 86 553 .668 640 553 1.498 .689 -.583 -.538
17 109 139 56 88 53 51 111 136 61 114 55 48 0 0 30 66 21 137 84 7 65 1 104 103 1.039 .962 .873 .925 1.033 4.664 52 233 7.666 .52 80 4210 7280 20 28 289 297 0 124 79 46 .859 121 43 1.164 .779 -.218 -.359
18 72 90 55 94 16 -3 72 84 60 112 17 -9 0 0 18 36 17 86 46 2 12 0 13 8 null null null 1.446 1.334 5.635 80 340 14.141 .14 100 4360 7280 19 29 303 313 -50 80 84 -3 null 75 -8 null null null null
19 382 306 59 92 322 213 374 281 61 102 315 188 0 0 160 112 15 55 100 98 100 86 535 503 1.512 .661 .597 .658 .647 2.445 52 243 .612 .79 80 4520 7280 20 28 320 328 0 273 82 190 .591 251 168 1.693 .533 -.759 -.908
20 1629 6262 63 103 1566 6158 1999 7371 69 132 1935 7267 0 0 791 2822 43 190 96 98 94 94 7724 9202 .254 3.932 3.756 4.401 3.876 2.233 52 217 3.867 .99 80 4660 7280 20 28 334 342 0 5593 92 5500 3.512 6584 6491 .285 3.354 1.812 1.746

Total number of rows: 44544

Table truncated, full table size 9686 Kbytes.




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