NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989676 Query DataSets for GSM989676
Status Public on Aug 23, 2012
Title PC 501T
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 501T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 555T
disease free survival: 24.20
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/2008-08/81178.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 2883 2383 51 130 2831 2252 3205 2598 56 147 3153 2467 0 0 1096 1046 22 80 100 100 100 94 5083 5620 1.257 .795 .782 .733 .813 3.264 52 292 .807 .97 80 1750 7950 31 39 39 47 0 1867 102 1764 .623 2035 1933 1.605 .613 -.682 -.706
2 3021 2536 51 126 2969 2410 3585 2764 56 140 3533 2637 0 0 1307 1088 27 70 100 96 100 92 5379 6170 1.232 .812 .746 .745 .791 2.997 52 263 .804 .98 80 1890 7950 31 39 53 61 0 1987 99 1888 .636 2166 2066 1.572 .585 -.653 -.774
3 4205 7640 54 136 4150 7504 4329 7864 59 147 4275 7728 0 0 493 1277 28 81 100 100 100 100 11654 12003 .553 1.808 1.808 1.789 1.808 2.249 32 221 1.851 .98 70 2040 7950 31 38 68 75 0 5986 107 5879 1.417 6161 6055 .706 1.416 .503 .502
4 3863 3275 49 120 3814 3154 4672 3671 53 130 4623 3551 0 0 1858 1537 17 63 100 98 100 98 6968 8174 1.209 .827 .768 .832 .821 3.809 52 252 .808 .97 80 2190 7950 31 39 83 91 0 2566 94 2471 .648 2876 2782 1.543 .602 -.626 -.733
5 179 133 50 123 128 9 191 118 55 130 141 -5 0 0 55 53 21 59 96 17 90 5 137 136 14.222 .07 null .366 .375 5.669 52 220 .039 .03 80 2340 7950 31 39 98 106 0 104 96 7 .055 92 -4 18.153 null -4.182 null
6 1641 2359 53 128 1587 2231 1666 2411 58 140 1612 2283 0 0 279 431 20 68 100 100 100 100 3818 3895 .711 1.406 1.416 1.4 1.426 2.391 52 231 1.41 .98 80 2500 7950 31 39 114 122 0 1848 100 1748 1.101 1889 1789 .908 1.11 .139 .15
7 94 143 53 132 41 11 95 125 56 149 41 -7 0 0 34 81 18 77 68 16 51 3 52 34 3.727 .268 null 1.849 2.351 10.618 80 319 25.98 .04 100 2640 7950 30 40 127 137 -50 112 103 9 .21 98 -5 4.757 null -2.25 null
8 4580 8760 55 147 4524 8613 5505 9955 58 164 5449 9807 0 0 1793 3067 17 80 100 100 100 100 13137 15256 .525 1.904 1.8 2.016 1.874 2.704 52 192 1.855 .98 80 2790 7950 31 39 143 151 0 6863 115 6748 1.492 7800 7684 .67 1.41 .577 .496
9 63 120 56 174 7 -53 61 102 61 192 4 -71 0 0 18 106 24 95 16 2 2 2 -46 -67 null null null 7.17 8.806 5.823 80 289 7.847 .44 100 2940 7940 29 39 157 167 -50 94 136 -42 null 80 -56 null null null null
10 67 136 56 180 10 -43 66 113 61 198 9 -66 0 0 18 70 20 105 25 2 7 0 -33 -57 null null null 4.535 5.019 6.941 80 317 13.582 .27 100 3090 7940 29 39 172 182 -50 107 141 -34 null 89 -52 null null null null
11 135 323 55 171 80 151 135 326 59 185 80 154 0 0 23 84 18 95 96 71 93 28 231 234 .53 1.888 1.925 1.815 1.962 4.072 32 202 4.239 .47 70 3250 7940 30 37 189 196 0 253 134 118 1.479 255 121 .676 1.508 .564 .593
12 133 327 55 161 78 166 136 323 60 180 81 161 0 0 34 130 18 90 94 71 88 44 244 242 .47 2.128 1.988 1.973 1.954 5.842 52 246 3.889 .59 80 3400 7940 30 38 204 212 0 256 126 130 1.667 253 126 .6 1.557 .738 .639
13 121 171 54 167 66 4 121 160 58 181 66 -7 0 0 27 70 17 87 93 15 87 0 70 59 16.5 .061 null .592 .679 6.381 32 175 21.126 .03 70 3540 7950 31 38 218 225 0 134 131 3 .047 125 -5 21.06 null -4.396 null
14 83 144 60 184 22 -39 75 113 68 215 14 -70 0 0 34 108 31 144 26 5 8 3 -17 -56 null null null 5.127 6.52 8.307 80 307 5.476 .51 100 3690 7940 29 39 232 242 -50 113 144 -31 null 89 -55 null null null null
15 56 153 59 189 -3 -36 48 83 67 219 -11 -106 0 0 39 306 32 157 5 3 3 2 -39 -117 null null null 8.603 8.266 5.363 80 308 8.267 .73 100 3840 7940 29 39 247 257 -50 120 148 -28 null 65 -83 null null null null
16 267 417 53 156 214 261 309 413 56 170 255 257 0 0 103 136 15 80 96 92 96 75 475 512 .82 1.22 1.008 1.312 1.197 3.7 52 212 1.228 .82 80 4000 7940 30 38 264 272 0 327 122 204 .956 324 201 1.047 .79 -.066 -.341
17 57 111 52 160 4 -49 54 87 56 174 1 -73 0 0 13 74 20 85 10 6 2 2 -45 -72 null null null 7.932 9.59 6.641 80 289 8.101 .47 100 4150 7930 28 38 278 288 -50 87 125 -38 null 68 -57 null null null null
18 51 120 53 166 -1 -45 48 97 58 187 -4 -68 0 0 15 92 22 106 6 3 3 3 -46 -72 null null null 6.709 6.526 6.122 80 273 12.701 .33 100 4300 7930 28 38 293 303 -50 94 130 -35 null 76 -53 null null null null
19 98 133 52 163 45 -29 99 126 56 181 46 -36 0 0 36 49 17 97 71 1 58 0 16 10 null null null 1.913 2.529 9.89 80 333 6.097 .2 100 4450 7930 28 38 308 318 -50 104 128 -23 null 99 -28 null null null null
20 565 1703 53 149 511 1554 616 1748 57 182 563 1599 0 0 157 447 19 241 100 100 100 98 2065 2162 .329 3.041 2.84 3.113 3.058 2.68 52 205 3.234 .91 80 4610 7940 30 38 325 333 0 1334 117 1218 2.383 1370 1253 .42 2.225 1.253 1.154

Total number of rows: 44544

Table truncated, full table size 9549 Kbytes.




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