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Sample GSM989772 Query DataSets for GSM989772
Status Public on Aug 23, 2012
Title PC 448T
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 448T2
Organism Homo sapiens
Characteristics ethnicity: African American
age: 71
pre-operation treatment: None
individual: PC 629T
disease free survival: 20.50
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/2008-08/81179.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 6475 7964 55 97 6419 7866 6876 8515 70 128 6820 8417 0 0 1882 2810 64 175 100 98 100 98 14285 15237 .816 1.225 1.234 1.099 1.269 3.926 52 367 1.228 .96 90 1740 7890 16 25 41 50 0 6617 81 6535 1.018 7074 6993 .982 1.025 .026 .036
2 6210 7875 55 96 6154 7779 7087 8665 62 112 7031 8569 0 0 2427 2626 25 69 100 100 100 100 13933 15600 .791 1.264 1.219 1.377 1.28 2.763 52 287 1.217 .97 90 1890 7900 17 26 56 65 0 6543 80 6463 1.05 7199 7119 .952 1.013 .071 .018
3 5782 10444 58 100 5723 10344 6252 11547 64 118 6193 11446 0 0 1583 2785 38 76 100 100 100 100 16067 17639 .553 1.807 1.848 1.846 1.831 2.727 52 228 1.799 .97 80 2040 7900 18 26 72 80 0 8677 83 8594 1.502 9593 9510 .666 1.536 .587 .619
4 5009 6348 53 93 4956 6255 6833 8227 62 114 6779 8134 0 0 4090 5197 42 79 78 83 76 75 11211 14913 .792 1.262 1.2 1.379 1.291 4.607 80 383 1.238 .97 100 2180 7890 16 26 85 95 0 5274 77 5197 1.049 6835 6758 .954 .997 .068 -.005
5 379 193 57 92 322 101 402 196 63 111 345 104 0 0 112 79 25 71 100 61 96 28 423 449 3.188 .314 .301 .304 .326 4.579 52 289 .265 .47 90 2350 7890 16 25 102 111 0 160 76 84 .261 163 86 3.837 .25 -1.94 -1.997
6 2571 4116 71 112 2500 4003 2777 4486 79 133 2706 4373 0 0 768 1321 39 78 100 100 100 100 6503 7079 .625 1.601 1.616 1.58 1.586 2.922 52 279 1.579 .96 90 2490 7890 16 25 116 125 0 3420 93 3326 1.33 3727 3633 .752 1.343 .412 .425
7 214 199 55 94 159 104 203 190 62 110 148 96 0 0 46 72 28 64 100 65 100 31 263 244 1.529 .654 .649 .629 .706 4.589 32 218 .546 .45 70 2640 7890 17 24 132 139 0 165 78 86 .543 158 80 1.84 .539 -.88 -.892
8 7250 12986 55 96 7194 12889 7817 14522 63 117 7761 14426 0 0 1618 3561 29 94 100 100 100 100 20083 22187 .558 1.792 1.859 1.753 1.88 2.678 52 253 1.809 .97 80 2790 7890 17 25 147 155 0 10789 80 10708 1.489 12065 11985 .672 1.544 .574 .627
9 106 132 54 90 51 41 98 126 59 107 43 36 0 0 49 64 22 79 66 18 48 6 92 79 1.244 .804 .837 1.06 1.209 6.888 80 355 1.571 .33 100 2940 7890 16 26 161 171 -50 110 75 34 .668 105 30 1.497 .696 -.582 -.524
10 116 151 53 90 63 61 112 153 59 107 59 62 0 0 39 66 43 69 69 40 26 9 124 121 1.033 .968 1.051 1.193 1.269 7.837 52 288 .83 .49 90 3090 7890 16 25 176 185 0 125 75 51 .804 127 52 1.243 .873 -.314 -.196
11 202 402 53 86 149 316 192 356 58 96 139 270 0 0 60 193 30 54 100 96 94 94 465 409 .472 2.121 1.942 1.953 2.156 3.845 52 241 2.475 .75 80 3250 7890 17 25 193 201 0 334 71 263 1.762 296 224 .568 1.614 .817 .69
12 226 490 53 96 172 394 236 464 63 114 182 368 0 0 67 163 38 79 96 96 86 92 566 550 .437 2.291 2.022 2.344 2.356 3.211 52 273 2.408 .88 80 3400 7890 17 25 208 216 0 407 80 327 1.903 385 306 .525 1.68 .928 .748
13 187 209 51 89 136 119 176 193 55 100 124 104 0 0 60 114 20 55 100 62 100 46 255 228 1.143 .875 .839 .656 .989 7.58 32 218 .949 .59 70 3550 7880 16 23 223 230 0 174 74 99 .727 160 86 1.376 .697 -.46 -.521
14 141 150 51 86 89 64 142 133 55 97 91 47 0 0 30 78 19 51 100 43 96 21 153 138 1.391 .719 .516 .515 .654 6.208 32 202 .956 .39 70 3700 7880 16 23 238 245 0 125 71 53 .597 110 39 1.674 .429 -.743 -1.221
15 65 76 52 96 13 -19 63 66 59 107 10 -29 0 0 20 40 26 57 22 3 3 2 -6 -19 null null null 3.019 3.077 7.065 80 376 4.993 .12 100 3850 7880 15 25 252 262 -50 63 80 -16 null 55 -24 null null null null
16 462 761 54 92 408 669 489 733 60 103 434 641 0 0 150 203 23 64 98 100 98 100 1077 1075 .61 1.64 1.477 1.797 1.645 3.294 52 274 1.589 .92 90 4000 7890 16 25 267 276 0 632 76 556 1.362 609 533 .734 1.227 .446 .295
17 111 151 53 89 58 62 111 150 59 98 58 61 0 0 36 61 25 50 81 53 53 25 120 119 .935 1.069 1.052 1.42 1.088 7.279 32 197 1.384 .36 70 4150 7880 16 23 283 290 0 125 74 52 .888 125 51 1.126 .874 -.171 -.195
18 79 104 53 89 26 15 65 92 60 103 12 2 0 0 46 54 29 58 31 16 15 3 41 14 1.733 .577 .167 2.001 1.758 11.701 80 335 1.105 .26 100 4300 7880 15 25 297 307 -50 86 74 12 .479 76 2 2.086 .138 -1.061 -2.852
19 201 259 50 94 150 164 173 262 60 111 122 167 0 0 187 94 30 66 100 86 94 59 314 289 .915 1.093 1.369 1.125 1.303 4.184 52 283 .576 .5 90 4460 7880 15 24 313 322 0 215 78 136 .908 218 139 1.101 1.137 -.139 .186
20 876 3941 55 97 820 3843 971 4370 62 115 915 4272 0 0 291 1459 27 78 100 98 100 98 4663 5187 .213 4.687 4.669 4.594 4.655 3.032 52 241 4.856 .96 80 4600 7880 16 24 328 336 0 3274 81 3193 3.894 3631 3549 .257 3.879 1.961 1.956

Total number of rows: 44544

Table truncated, full table size 9444 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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