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Sample GSM989699 Query DataSets for GSM989699
Status Public on Aug 23, 2012
Title PC 405T
Sample type RNA
 
Channel 1
Source name Human 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 405T
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 58
pre-operation treatment: None
individual: PC 335T
disease free survival: 45.47
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/2008-08/80899.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 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 3094 2017 81 63 3013 1954 3744 2269 85 73 3663 2206 0 0 1246 975 27 45 100 98 100 98 4967 5869 1.542 .649 .602 .547 .648 2.302 52 310 .656 .94 80 1950 7020 46 54 43 51 0 2168 68 2100 .697 2439 2371 1.435 .647 -.521 -.627
2 2937 1990 86 55 2851 1935 3518 2295 92 67 3432 2240 0 0 1623 1078 33 46 100 98 98 94 4786 5672 1.473 .679 .653 .678 .64 3.473 52 280 .656 .93 80 2100 7010 45 53 58 66 0 2139 59 2080 .73 2467 2408 1.371 .702 -.455 -.511
3 3187 4821 87 72 3100 4749 3976 6409 95 83 3889 6337 0 0 1714 2649 34 49 100 96 98 96 7849 10226 .653 1.532 1.629 1.344 1.496 3.029 52 267 1.569 .95 80 2250 7010 45 53 73 81 0 5182 77 5105 1.647 6889 6811 .607 1.751 .72 .809
4 3714 3007 87 65 3627 2942 3834 3186 92 74 3747 3121 0 0 902 886 32 45 100 100 100 100 6569 6868 1.233 .811 .833 .778 .85 1.406 52 236 .818 .96 80 2400 7010 45 53 88 96 0 3232 70 3162 .872 3425 3355 1.147 .895 -.198 -.16
5 160 56 86 61 74 -5 148 44 92 69 62 -17 0 0 67 34 33 45 67 7 48 0 69 45 null null null .563 .42 4.487 52 260 .043 .03 90 2550 7010 44 53 102 111 -50 60 66 -5 null 47 -18 null null null null
6 1219 2445 90 78 1129 2367 1274 2620 98 89 1184 2542 0 0 365 707 35 53 100 100 100 100 3496 3726 .477 2.097 2.147 2.113 2.12 1.808 52 219 2.174 .93 80 2700 7010 45 53 118 126 0 2628 84 2544 2.253 2816 2732 .444 2.308 1.172 1.206
7 124 66 85 59 39 7 114 53 91 70 29 -6 0 0 45 41 31 49 46 17 26 3 46 23 5.571 .179 null 1.205 1.427 4.655 52 264 11.543 .04 90 2850 7010 44 53 132 141 -50 71 63 8 .193 57 -6 5.183 null -2.374 null
8 3454 4797 81 62 3373 4735 4196 5997 87 70 4115 5935 0 0 1714 2391 30 48 100 100 98 100 8108 10050 .712 1.404 1.442 1.498 1.369 2.414 52 226 1.423 .96 80 3010 7010 45 53 149 157 0 5156 67 5089 1.509 6446 6379 .663 1.55 .593 .633
9 115 77 78 67 37 10 117 74 84 76 39 7 0 0 33 35 31 45 57 17 21 1 47 46 3.7 .27 .179 .794 .667 3.038 52 272 8.2 .09 90 3160 7000 43 52 163 172 -50 83 72 11 .291 80 8 3.442 .193 -1.783 -2.374
10 112 73 82 52 30 21 104 69 90 70 22 17 0 0 37 42 63 103 13 3 1 0 51 39 1.429 .7 .773 .949 .907 3.83 52 282 1.872 .8 90 3310 7000 43 52 178 187 -50 78 56 23 .752 74 18 1.329 .831 -.41 -.268
11 173 220 81 66 92 154 162 197 96 73 81 131 0 0 53 102 90 45 44 88 9 73 246 212 .597 1.674 1.617 1.742 1.725 2.712 52 234 .369 .27 80 3470 7000 44 52 195 203 0 236 71 166 1.799 212 141 .556 1.738 .847 .798
12 149 284 78 69 71 215 149 273 83 74 71 204 0 0 48 102 26 41 82 96 59 94 286 275 .33 3.028 2.873 3.511 2.999 2.646 52 226 3.838 .59 80 3610 7010 45 53 209 217 0 305 74 231 3.255 293 219 .307 3.088 1.703 1.627
13 151 92 84 60 67 32 147 83 91 78 63 23 0 0 41 50 47 104 65 9 28 0 99 86 2.094 .478 .365 .525 .537 5.097 32 164 1.478 .09 60 3770 7000 45 51 226 232 0 99 64 34 .513 89 25 1.948 .392 -.962 -1.35
14 125 121 79 69 46 52 121 96 87 85 42 27 0 0 41 90 44 93 48 19 11 11 98 69 .885 1.13 .643 1.02 1.333 4.896 52 220 7.934 .17 80 3910 7010 45 53 239 247 0 130 74 56 1.215 103 29 .823 .691 .281 -.533
15 115 57 76 61 39 -4 111 51 82 71 35 -10 0 0 31 27 32 45 50 7 19 0 35 25 null null null .501 .618 4.591 52 264 4.814 .08 90 4060 7000 43 52 253 262 -50 61 66 -4 null 55 -11 null null null null
16 371 177 79 59 292 118 366 162 92 88 287 103 0 0 126 96 95 141 94 28 78 5 410 390 2.475 .404 .359 .348 .394 2.547 52 236 .728 .71 80 4220 7000 44 52 270 278 0 190 63 127 .434 174 111 2.302 .386 -1.203 -1.374
17 307 80 79 68 228 12 133 73 84 83 54 5 0 0 671 35 34 56 68 12 37 0 240 59 19 .053 .093 .591 .737 4.033 32 158 .094 .12 60 4370 7000 45 51 286 292 0 86 73 13 .057 78 5 17.677 .1 -4.144 -3.329
18 103 61 79 55 24 6 96 56 84 66 17 1 0 0 28 31 31 53 40 9 9 0 30 18 4 .25 .059 1.299 2.4 6.009 52 285 8.776 .12 90 4520 6990 42 51 299 308 -50 66 59 6 .269 60 1 3.721 .063 -1.896 -3.983
19 150 105 80 60 70 45 143 94 87 76 63 34 0 0 55 64 33 70 69 30 48 7 115 97 1.556 .643 .54 .86 .944 3.611 52 282 1.777 .45 90 4670 6990 42 51 314 323 -50 113 64 48 .691 101 37 1.447 .58 -.533 -.786
20 576 1197 84 64 492 1133 626 1317 90 90 542 1253 0 0 278 443 36 176 90 94 88 92 1625 1795 .434 2.303 2.312 2.856 2.374 2.236 52 256 2.145 .67 80 4830 6990 43 51 331 339 0 1287 69 1218 2.475 1416 1347 .404 2.485 1.308 1.313

Total number of rows: 44544

Table truncated, full table size 9404 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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