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Sample GSM989680 Query DataSets for GSM989680
Status Public on Aug 23, 2012
Title TB 1872T
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 TB 1872T2
Organism Homo sapiens
Characteristics age: 57
individual: TB 2682T
disease state: Positive
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/2008-08/81140.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 24389 16287 98 168 24290 16118 31381 19385 107 211 31282 19217 0 0 17674 7142 47 217 98 98 92 98 40408 50499 1.507 .664 .614 1.226 .555 6.641 52 371 .517 .87 90 1850 7310 46 55 24 33 0 14395 148 14246 .586 17133 16985 1.705 .543 -.77 -.881
2 24681 15271 101 167 24580 15104 34052 17153 113 219 33951 16986 0 0 16371 5512 52 256 100 100 98 100 39684 50937 1.627 .614 .5 1.151 .503 7.838 52 311 .482 .89 90 2000 7310 46 55 39 48 0 13497 148 13350 .543 15161 15013 1.841 .442 -.881 -1.177
3 23338 15932 103 164 23235 15767 28620 21015 122 215 28517 20850 0 0 17070 9142 71 187 88 88 82 88 39002 49367 1.474 .679 .731 1.05 .606 5.04 52 299 .603 .92 90 2150 7310 46 55 54 63 0 14081 145 13936 .6 18574 18428 1.667 .646 -.738 -.63
4 26784 16415 111 180 26673 16234 35643 18435 126 222 35532 18254 0 0 15622 5084 61 172 98 100 92 100 42907 53786 1.643 .609 .514 1.117 .516 7.979 52 325 .498 .89 90 2300 7310 46 55 69 78 0 14508 159 14348 .538 16294 16134 1.859 .454 -.894 -1.139
5 2861 1122 124 221 2736 901 2895 1154 135 248 2770 933 0 0 415 251 56 142 100 100 100 100 3637 3703 3.037 .329 .337 .319 .33 1.943 32 195 .307 .78 70 2460 7310 47 54 86 93 0 992 195 796 .291 1020 825 3.436 .298 -1.781 -1.748
6 9467 21346 143 269 9323 21077 1701 11648 160 306 1558 11379 0 0 10818 19480 69 258 100 100 100 97 30400 12937 .442 2.261 7.304 2.823 2.016 3.436 120 505 2.031 .89 120 2600 7310 45 57 98 110 0 18867 238 18629 1.998 10295 10057 .5 6.455 .999 2.69
7 718 503 125 242 593 260 707 533 138 297 581 290 0 0 141 129 52 376 100 12 100 0 853 871 2.281 .438 .499 .44 .524 2.439 32 167 .417 .52 60 2760 7310 48 54 117 123 0 445 214 230 .388 471 256 2.58 .441 -1.368 -1.181
8 26714 19475 107 178 26607 19297 36739 24276 118 208 36632 24097 0 0 18991 9167 53 145 96 100 94 96 45904 60729 1.379 .725 .658 1.421 .619 6.112 52 332 .596 .9 90 2910 7300 45 54 130 139 0 17213 157 17056 .641 21456 21298 1.56 .581 -.642 -.782
9 359 166 95 151 264 14 353 153 106 169 257 2 0 0 45 48 41 93 100 8 100 0 278 259 18.857 .053 .008 .141 .21 4.84 12 104 .138 .23 50 3060 7300 47 52 147 152 0 147 133 12 .047 135 2 21.335 .007 -4.415 -7.184
10 230 299 103 166 127 132 237 268 108 194 134 102 0 0 67 153 46 129 87 34 62 18 259 236 .962 1.039 .761 .993 .847 7.715 32 217 5.959 .14 70 3220 7310 47 54 162 169 0 264 147 117 .919 237 90 1.089 .673 -.122 -.572
11 1251 1946 94 177 1157 1768 1523 2045 103 215 1428 1868 0 0 701 808 51 155 90 98 86 92 2925 3296 .654 1.528 1.308 1.99 1.339 4.872 52 257 1.408 .84 80 3370 7310 47 55 177 185 0 1720 156 1563 1.351 1807 1651 .74 1.156 .434 .209
12 906 13863 92 187 813 13676 1051 13801 102 222 959 13614 0 0 424 3353 47 193 96 100 90 100 14489 14573 .059 16.822 14.196 21.869 13.686 4.153 52 305 17.919 .83 90 3510 7310 46 55 190 199 0 12253 165 12088 14.868 12198 12033 .067 12.547 3.894 3.649
13 880 377 87 157 792 220 878 393 98 201 790 236 0 0 125 108 38 139 100 75 100 34 1012 1026 3.6 .278 .299 .239 .287 3.045 32 221 .252 .47 70 3670 7310 47 54 207 214 0 333 139 194 .246 347 209 4.073 .264 -2.026 -1.921
14 329 446 92 167 236 279 329 422 100 199 236 254 0 0 69 219 39 172 100 75 100 18 515 490 .846 1.182 1.076 1.009 1.113 3.441 32 202 1.783 .56 70 3820 7310 47 54 222 229 0 394 148 247 1.045 373 224 .957 .951 .063 -.072
15 97 107 92 167 4 -60 95 92 99 209 3 -75 0 0 25 80 39 236 7 1 0 0 -56 -72 null null null 3.606 3.68 7.699 52 308 26.614 .2 90 3960 7300 45 54 235 244 -50 95 148 -53 null 81 -66 null null null null
16 3117 2644 87 162 3030 2481 3910 2791 98 216 3822 2629 0 0 1830 837 54 289 96 100 88 98 5511 6451 1.221 .819 .688 1.384 .717 6.358 52 264 .653 .86 80 4110 7300 46 54 251 259 0 2337 143 2193 .724 2467 2324 1.382 .608 -.467 -.718
17 143 262 92 162 51 99 129 246 104 209 37 83 0 0 63 110 62 180 34 17 7 3 150 120 .515 1.941 2.243 1.868 1.419 6.756 52 301 9.018 .18 90 4260 7300 45 54 265 274 -50 232 143 88 1.716 217 73 .583 1.983 .779 .987
18 102 112 99 194 2 -82 95 96 109 236 -4 -98 0 0 32 57 56 158 7 0 0 0 -80 -102 null null null 5.087 5.206 6.136 52 319 11.783 .22 90 4420 7300 45 54 281 290 -50 99 171 -72 null 85 -87 null null null null
19 1137 1435 98 182 1038 1253 1166 1418 107 231 1068 1235 0 0 489 388 43 176 96 100 88 100 2291 2303 .828 1.207 1.156 1.597 1.069 4.896 52 271 1.114 .81 80 4570 7300 46 54 297 305 0 1268 161 1107 1.067 1253 1092 .937 1.022 .093 .031
20 6664 19181 111 217 6553 18963 8640 20637 124 281 8528 20419 0 0 4008 5256 56 194 100 100 96 100 25516 28947 .346 2.894 2.394 4.709 2.316 5.974 52 259 2.645 .87 80 4720 7300 46 54 312 320 0 16953 192 16760 2.558 18240 18047 .391 2.116 1.355 1.082

Total number of rows: 44544

Table truncated, full table size 9823 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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