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Sample GSM989756 Query DataSets for GSM989756
Status Public on Aug 23, 2012
Title PC 470T
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 470T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 72
pre-operation treatment: None
individual: PC 470T
disease free survival: 47.87
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/2008-08/81176.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 9144 11820 51 104 9093 11716 11449 14642 56 117 11397 14538 0 0 4981 7756 23 81 100 88 100 88 20809 25935 .776 1.288 1.276 .87 1.384 8.81 52 302 1.337 .9 80 1750 7780 22 30 39 47 0 10558 93 10465 1.151 13079 12986 .869 1.139 .203 .188
2 9898 12627 53 105 9844 12522 12390 14953 62 131 12336 14848 0 0 5529 8940 38 130 100 86 100 86 22366 27184 .786 1.272 1.204 .731 1.385 11.255 52 262 1.351 .91 80 1900 7780 22 30 54 62 0 11279 94 11185 1.136 13356 13263 .88 1.075 .184 .104
3 9452 21187 56 105 9396 21081 11727 25421 65 126 11671 25316 0 0 4667 13710 31 89 100 92 100 88 30477 36987 .446 2.244 2.169 1.381 2.545 9.829 52 266 2.506 .92 80 2050 7780 22 30 69 77 0 18925 94 18830 2.004 22707 22613 .499 1.938 1.003 .954
4 10186 12986 55 108 10131 12878 13439 15001 63 123 13383 14893 0 0 5361 8356 31 75 100 92 100 92 23009 28276 .787 1.271 1.113 .974 1.414 8.312 52 272 1.324 .91 80 2200 7780 22 30 84 92 0 11599 96 11503 1.135 13399 13303 .881 .994 .183 -.009
5 655 254 52 105 603 149 756 250 63 122 703 145 0 0 259 138 43 109 96 63 96 21 752 848 4.047 .247 .206 .225 .231 3.883 52 200 .26 .65 80 2360 7780 22 30 100 108 0 227 94 133 .221 223 130 4.531 .184 -2.18 -2.44
6 2996 5082 56 113 2939 4968 570 609 69 134 513 495 0 0 3288 6251 47 101 95 86 89 71 7907 1008 .592 1.69 .965 1.191 1.699 4.496 120 454 1.842 .94 120 2500 7790 21 33 112 124 0 4539 101 4438 1.51 544 442 .662 .862 .594 -.214
7 240 196 52 109 188 87 241 183 63 130 188 73 0 0 47 54 34 72 100 50 100 18 275 261 2.161 .463 .388 .374 .416 4.165 32 213 .565 .33 70 2650 7780 22 29 129 136 0 175 97 78 .413 163 65 2.419 .347 -1.275 -1.528
8 13874 28921 53 113 13820 28808 14032 34858 65 127 13979 34744 0 0 1699 13490 37 80 100 96 100 96 42628 48723 .48 2.085 2.485 1.17 2.385 9.859 32 234 2.512 .91 70 2800 7770 21 28 144 151 0 25833 101 25732 1.862 31136 31034 .537 2.22 .897 1.151
9 226 543 53 112 172 431 233 545 63 123 179 433 0 0 40 142 39 83 100 96 96 96 603 612 .399 2.506 2.419 2.43 2.281 2.769 32 210 2.822 .81 70 2950 7780 22 29 159 166 0 485 100 385 2.238 487 387 .447 2.161 1.162 1.111
10 210 406 51 102 159 303 215 394 60 116 163 291 0 0 55 100 32 64 100 100 90 96 462 454 .525 1.906 1.785 1.923 1.919 2.679 32 199 2.163 .68 70 3100 7780 22 29 174 181 0 363 91 271 1.702 352 260 .587 1.595 .767 .673
11 875 1913 53 108 822 1805 875 2138 59 123 822 2030 0 0 107 783 25 64 100 96 100 90 2627 2852 .455 2.196 2.47 1.864 2.416 4.067 32 222 2.717 .86 70 3250 7770 21 28 189 196 0 1709 96 1612 1.961 1910 1813 .51 2.206 .972 1.141
12 690 1354 53 117 636 1236 712 1549 61 133 658 1432 0 0 120 523 25 83 100 93 100 90 1872 2090 .515 1.943 2.176 1.568 2.062 5.285 32 229 2.199 .88 70 3400 7770 21 28 204 211 0 1209 105 1104 1.736 1384 1279 .576 1.944 .796 .959
13 442 545 59 133 382 412 442 560 80 163 382 427 0 0 54 217 158 143 100 87 90 78 794 809 .927 1.079 1.118 1.027 1.166 3.084 32 216 1.237 .78 70 3550 7770 21 28 219 226 0 487 119 368 .963 500 381 1.038 .998 -.054 -.002
14 175 312 67 146 107 166 185 312 83 193 117 166 0 0 43 80 58 271 87 9 50 0 273 283 .645 1.551 1.419 1.327 1.53 3.793 32 144 1.818 .58 60 3700 7780 23 29 235 241 0 279 130 148 1.386 279 148 .722 1.267 .471 .342
15 67 126 76 167 -9 -40 63 100 94 192 -12 -67 0 0 21 72 57 121 2 5 0 1 -49 -79 null null null 4.111 3.965 5.908 80 335 3.588 .48 100 3850 7770 20 30 248 258 -50 113 149 -36 null 89 -60 null null null null
16 834 1465 86 172 747 1292 1079 1623 103 200 993 1450 0 0 432 854 68 112 90 86 86 80 2039 2443 .578 1.73 1.46 1.504 1.853 5.049 52 234 1.821 .9 80 4000 7770 21 29 264 272 0 1309 154 1154 1.545 1450 1295 .647 1.304 .628 .383
17 157 344 81 168 75 175 157 366 120 217 75 197 0 0 28 69 114 181 0 58 0 0 250 272 .429 2.333 2.627 2.523 2.189 3.052 12 102 3.149 .36 50 4150 7770 22 27 280 285 0 307 150 156 2.084 327 176 .48 2.346 1.059 1.23
18 58 122 78 172 -19 -50 52 101 97 201 -25 -71 0 0 18 67 72 139 0 2 0 0 -69 -96 null null null 2.953 2.912 4.032 80 361 2.261 .41 100 4300 7760 19 29 293 303 -50 109 154 -45 null 90 -63 null null null null
19 708 863 60 142 647 721 706 983 71 155 645 841 0 0 153 344 40 80 100 90 100 87 1368 1486 .897 1.114 1.304 1.147 1.254 2.648 32 214 2.279 .73 70 4450 7760 20 27 309 316 0 771 127 644 .995 878 751 1.005 1.165 -.007 .22
20 3324 15837 62 143 3262 15693 3699 17996 72 166 3636 17852 0 0 1015 5353 41 110 100 100 100 96 18955 21488 .208 4.811 4.91 4.474 5.053 4.469 32 212 5.162 .91 70 4600 7770 21 28 324 331 0 14146 128 14017 4.297 16074 15946 .233 4.386 2.103 2.133

Total number of rows: 44544

Table truncated, full table size 9316 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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