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Sample GSM989739 Query DataSets for GSM989739
Status Public on Aug 23, 2012
Title PC 184N
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 184N2
Organism Homo sapiens
Characteristics individual: PC 184N
disease state: Normal
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/2008-08/81105.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) [email protected]
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 19513 19439 86 103 19427 19335 22252 19592 90 112 22165 19489 0 0 14903 14953 27 55 100 100 100 100 38762 41654 1.005 .995 .879 1.097 1.054 3.532 52 303 .985 .96 80 1780 6850 29 37 22 30 0 17273 92 17181 .884 17409 17318 1.131 .781 -.177 -.356
2 17784 16739 101 134 17683 16605 13888 14148 108 141 13787 14014 0 0 15576 14877 41 67 100 98 100 96 34288 27801 1.065 .939 1.016 .942 .992 3.861 52 276 .937 .97 80 1930 6840 28 36 37 45 0 14874 119 14755 .834 12572 12453 1.198 .903 -.261 -.147
3 27340 28421 112 148 27227 28272 26208 32218 129 156 26096 32069 0 0 20482 21235 62 77 100 100 100 100 55499 58165 .963 1.038 1.229 1.178 1.112 3.248 52 313 1.025 .96 90 2090 6840 27 36 52 61 0 25255 132 25122 .923 28629 28496 1.084 1.092 -.116 .127
4 22640 19693 111 136 22528 19556 28818 24566 135 160 28707 24430 0 0 12255 11448 77 109 100 92 98 92 42084 53137 1.152 .868 .851 .618 .875 4.297 52 308 .866 .95 90 2240 6830 26 35 67 76 0 17499 121 17377 .771 21829 21708 1.296 .756 -.375 -.403
5 1454 331 215 180 1238 150 1556 325 204 206 1340 144 0 0 427 109 95 111 100 62 96 28 1388 1484 8.253 .121 .107 .099 .131 5.35 32 164 .093 .45 60 2380 6830 28 34 83 89 0 294 160 133 .108 289 128 9.288 .095 -3.215 -3.388
6 8566 8150 172 175 8394 7974 1282 1676 197 199 1110 1500 0 0 9379 8984 102 102 100 100 100 100 16368 2610 1.053 .95 1.351 .938 .971 2.239 120 542 .948 .98 120 2540 6840 26 38 96 108 0 7242 156 7086 .844 1489 1333 1.185 1.201 -.244 .264
7 419 163 111 140 308 23 425 155 120 152 313 15 0 0 69 36 52 70 100 16 100 0 331 328 13.391 .075 .048 .084 .111 3.773 12 104 .146 .29 50 2690 6830 28 33 114 119 0 145 124 20 .066 138 13 15.07 .043 -3.914 -4.554
8 15467 14381 82 118 15385 14262 5251 6704 101 136 5168 6585 0 0 16693 15771 55 79 100 100 100 93 29647 11753 1.079 .927 1.274 .921 1.022 3.665 80 373 .93 .98 110 2840 6850 27 38 126 137 0 12779 105 12673 .824 5957 5851 1.214 1.132 -.28 .179
9 156 184 74 106 82 77 153 153 90 133 79 46 0 0 63 149 60 85 63 28 23 9 159 125 1.065 .939 .582 .855 .761 6.852 52 255 1.626 .54 90 2990 6840 27 36 142 151 -50 164 94 68 .834 136 41 1.198 .517 -.261 -.951
10 178 339 60 83 117 256 175 308 63 92 115 225 0 0 35 114 17 43 100 100 100 96 373 340 .457 2.188 1.957 2.08 2.223 2.219 32 195 2.484 .76 70 3140 6840 28 35 158 165 0 301 74 227 1.944 274 200 .514 1.739 .959 .798
11 1042 1706 60 91 981 1614 1092 1890 63 106 1031 1798 0 0 232 617 21 67 100 100 100 96 2595 2829 .608 1.645 1.744 1.486 1.92 2.415 32 225 1.767 .9 70 3290 6830 27 34 173 180 0 1516 81 1434 1.462 1679 1598 .684 1.55 .548 .632
12 461 1395 59 89 401 1306 470 1491 63 108 410 1401 0 0 95 452 21 105 100 100 100 100 1707 1811 .307 3.257 3.417 3.057 3.302 2.066 32 226 3.691 .93 70 3450 6830 27 34 189 196 0 1240 79 1161 2.894 1325 1245 .346 3.036 1.533 1.602
13 510 393 59 84 450 308 533 390 63 99 473 306 0 0 104 123 18 62 100 96 100 90 758 779 1.461 .684 .647 .596 .658 2.994 32 229 .693 .87 70 3590 6820 26 33 203 210 0 349 75 274 .608 347 272 1.644 .575 -.717 -.799
14 359 500 55 81 303 418 393 504 59 100 337 422 0 0 107 230 17 72 100 96 100 90 721 759 .725 1.38 1.252 1.361 1.213 2.569 32 169 1.614 .73 60 3740 6830 28 34 219 225 0 444 72 371 1.226 448 375 .816 1.113 .294 .154
15 71 84 61 90 10 -5 69 61 64 115 8 -28 0 0 23 74 19 81 25 5 3 3 5 -20 null null null 4.927 4.816 8.909 52 327 7.569 .37 90 3890 6820 25 34 232 241 -50 75 80 -4 null 54 -25 null null null null
16 2956 2473 63 103 2893 2370 3717 2980 66 121 3654 2877 0 0 1478 1237 17 68 100 94 100 92 5263 6531 1.221 .819 .787 .707 .796 3.781 52 275 .802 .95 80 4050 6820 26 34 249 257 0 2198 92 2106 .728 2648 2556 1.374 .7 -.458 -.515
17 102 283 59 92 42 191 106 278 64 123 46 185 0 0 27 87 29 194 62 43 31 0 233 231 .22 4.548 4.022 4.746 4.177 4.352 32 185 5.53 .56 70 4190 6840 28 35 263 270 0 251 82 170 4.041 247 164 .247 3.574 2.015 1.837
18 61 77 57 90 4 -13 58 66 60 102 0 -23 0 0 13 39 19 59 11 7 1 0 -9 -23 null null null 3.596 3.509 4.744 52 315 8.931 .24 90 4340 6830 26 35 277 286 -50 68 80 -12 null 59 -20 null null null null
19 659 455 58 91 600 363 744 457 62 103 685 365 0 0 311 231 17 60 100 86 96 82 963 1050 1.653 .605 .533 .597 .587 3.553 52 294 .576 .81 80 4500 6820 26 34 294 302 0 404 81 323 .538 406 324 1.86 .473 -.895 -1.079
20 3609 11664 61 104 3547 11559 3663 12706 64 119 3602 12601 0 0 621 3225 21 71 100 100 100 100 15106 16203 .307 3.259 3.498 3.074 3.413 2.035 32 213 3.436 .96 70 4650 6830 27 34 309 316 0 10365 92 10271 2.896 11291 11197 .345 3.109 1.534 1.636

Total number of rows: 44544

Table truncated, full table size 9520 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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