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Sample GSM989736 Query DataSets for GSM989736
Status Public on Aug 23, 2012
Title PC 601T
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 601T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 646T
disease free survival: 16.60
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/2008-09/81290.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 GPL15971
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 6303 6359 49 53 6254 6306 6618 6270 51 63 6569 6216 0 0 3083 3030 14 40 100 100 100 98 12560 12785 .992 1.008 .946 1.099 .961 3.677 80 401 .977 .93 100 1800 6780 21 31 35 45 0 5658 47 5611 .897 5579 5531 1.115 .842 -.157 -.248
2 4947 4739 54 66 4893 4673 5188 4901 59 80 5134 4835 0 0 3077 3078 16 62 100 96 98 90 9566 9969 1.047 .955 .942 .971 .925 5.231 80 262 .951 .94 100 1950 6780 21 31 50 60 0 4217 59 4158 .85 4361 4302 1.177 .838 -.235 -.255
3 6939 13099 59 82 6880 13016 6988 13435 64 105 6929 13352 0 0 2969 5890 56 173 98 98 98 96 19896 20281 .529 1.892 1.927 1.791 1.835 3.418 80 340 1.92 .94 110 2100 6770 19 30 64 75 0 11655 73 11581 1.683 11954 11880 .594 1.715 .751 .778
4 3418 3300 60 79 3358 3221 3563 3352 72 102 3503 3273 0 0 1377 1383 61 166 96 97 91 93 6579 6776 1.043 .959 .934 1.11 .941 3.124 80 359 .943 .92 100 2250 6780 21 31 80 90 0 2936 70 2866 .853 2983 2912 1.172 .831 -.229 -.266
5 492 219 65 100 427 119 443 196 79 121 377 95 0 0 180 122 44 86 98 53 97 31 546 472 3.588 .279 .252 .215 .285 4.185 80 443 .315 .57 110 2410 6780 20 31 95 106 0 195 89 106 .248 174 85 4.033 .224 -2.012 -2.157
6 9046 9826 76 114 8970 9711 9080 9467 91 134 9003 9353 0 0 2182 2481 51 86 100 100 100 100 18681 18356 .924 1.083 1.039 1.088 1.064 1.735 80 387 1.077 .97 110 2550 6780 20 31 109 120 0 8743 101 8641 .963 8423 8322 1.038 .924 -.054 -.113
7 274 337 66 95 208 241 267 315 76 109 200 219 0 0 67 178 35 66 100 88 100 76 449 419 .863 1.159 1.095 1.024 1.281 2.954 52 247 1.47 .67 90 2710 6770 20 29 126 135 0 300 85 214 1.031 280 195 .97 .974 .044 -.038
8 23585 48170 66 108 23518 48061 24620 48880 76 124 24553 48771 0 0 4879 7858 39 75 100 100 100 100 71579 73324 .489 2.044 1.986 2.104 2.025 1.798 80 298 2.021 .97 110 2850 6780 20 31 139 150 0 42860 96 42763 1.818 43492 43395 .55 1.767 .863 .822
9 269 266 59 105 210 160 278 188 71 117 219 82 0 0 105 490 46 69 91 56 87 27 370 301 1.313 .762 .374 .49 .499 5.715 80 306 4.031 .44 110 3010 6770 19 30 155 166 0 237 93 142 .678 167 73 1.475 .333 -.561 -1.586
10 311 361 58 93 252 268 312 353 60 106 253 260 0 0 84 160 19 57 97 90 96 85 520 513 .94 1.063 1.028 .92 .98 3.75 80 330 1.223 .78 110 3160 6770 19 30 170 181 0 321 83 238 .946 314 231 1.057 .914 -.08 -.129
11 1578 2808 61 95 1517 2712 1590 2704 64 102 1528 2608 0 0 567 1171 20 52 100 100 100 98 4229 4136 .559 1.788 1.707 1.702 1.772 2.345 80 349 1.876 .95 110 3310 6770 19 30 185 196 0 2498 85 2413 1.591 2406 2321 .629 1.519 .67 .603
12 931 3017 59 101 871 2916 920 2915 61 113 860 2813 0 0 227 897 17 65 100 100 100 100 3787 3673 .299 3.348 3.271 3.304 3.274 1.82 80 310 3.623 .93 110 3460 6780 20 31 200 211 0 2684 90 2595 2.979 2594 2503 .336 2.91 1.575 1.541
13 673 424 56 99 617 325 669 419 58 111 613 320 0 0 165 165 16 62 100 95 100 90 942 933 1.898 .527 .522 .487 .526 2.327 80 308 .57 .86 110 3610 6770 19 30 215 226 0 377 88 289 .469 373 285 2.134 .464 -1.093 -1.106
14 388 592 56 93 332 499 383 574 59 98 326 481 0 0 95 177 16 49 100 100 100 100 831 807 .665 1.503 1.475 1.503 1.535 2.215 80 208 1.577 .86 100 3750 6780 21 31 230 240 0 527 83 444 1.337 511 428 .748 1.313 .419 .393
15 71 68 58 100 13 -31 69 50 61 112 10 -49 0 0 16 47 20 56 30 5 5 2 -18 -39 null null null 4.003 5.991 6.793 120 365 -34.407 -.06 120 3900 6770 19 31 244 256 -100 61 89 -28 null 44 -44 null null null null
16 2272 3923 59 93 2213 3830 2214 3752 62 111 2155 3658 0 0 616 1247 21 68 100 100 100 100 6043 5813 .578 1.731 1.697 1.704 1.74 1.787 80 293 1.782 .96 110 4060 6770 19 30 260 271 0 3491 83 3408 1.54 3338 3255 .649 1.51 .623 .595
17 237 295 59 99 178 196 229 263 85 196 169 164 0 0 66 128 202 918 27 0 0 0 374 333 .908 1.101 .97 .936 .958 3.031 80 252 1.264 .73 110 4210 6770 19 30 275 286 0 262 88 174 .98 234 146 1.021 .863 -.03 -.212
18 67 76 60 104 7 -27 64 66 61 113 4 -37 0 0 24 47 19 62 19 6 2 0 -20 -33 null null null 4.032 6.433 8.17 120 313 -1 -1 120 4360 6770 19 31 290 302 -100 68 93 -24 null 59 -33 null null null null
19 897 1270 60 101 836 1168 916 1216 62 113 855 1115 0 0 496 742 19 62 95 92 89 90 2004 1970 .716 1.397 1.304 1.54 1.434 3.083 120 335 1.443 .93 120 4510 6770 19 31 305 317 0 1130 90 1039 1.243 1082 992 .804 1.16 .314 .215
20 4712 20533 61 109 4650 20423 4770 20138 64 117 4708 20028 0 0 1128 4837 17 62 100 100 100 100 25073 24736 .228 4.392 4.254 4.467 4.191 1.862 80 282 4.516 .96 110 4660 6770 19 30 320 331 0 18270 97 18172 3.908 17918 17820 .256 3.785 1.966 1.92

Total number of rows: 44544

Table truncated, full table size 9575 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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