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Sample GSM989757 Query DataSets for GSM989757
Status Public on Aug 23, 2012
Title PC 111T
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 PT 111
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 50
pre-operation treatment: None
individual: PC 37T
disease free survival: 40.57
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/2008-11/81783.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 GPL15972
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 12434 7813 46 101 12388 7711 13246 8094 50 125 13199 7992 0 0 2691 1402 17 107 100 100 100 100 20099 21191 1.607 .622 .606 .631 .613 2.266 52 356 .589 .96 90 1560 7640 31 40 19 28 0 6531 84 6446 .52 6766 6681 1.922 .506 -.942 -.982
2 12093 8467 47 111 12046 8356 12853 8991 50 120 12805 8880 0 0 2666 1549 17 62 100 100 100 100 20402 21685 1.442 .694 .693 .704 .697 2.285 52 276 .66 .96 90 1710 7640 31 40 34 43 0 7078 93 6985 .58 7516 7423 1.724 .58 -.786 -.787
3 5817 13842 49 108 5768 13733 6169 15071 52 129 6120 14963 0 0 1349 3349 19 97 100 100 100 100 19501 21083 .42 2.381 2.445 2.369 2.425 2.43 52 328 2.399 .96 90 1860 7630 30 39 49 58 0 11571 90 11480 1.99 12599 12509 .502 2.044 .993 1.031
4 13165 7545 54 117 13110 7427 13591 7783 88 172 13536 7665 0 0 2117 2200 105 187 100 100 100 100 20537 21201 1.765 .567 .566 .531 .586 2.517 52 285 .568 .96 90 2020 7630 30 39 65 74 0 6307 98 6209 .474 6506 6408 2.112 .473 -1.078 -1.079
5 257 198 65 141 191 56 252 179 106 183 186 38 0 0 80 108 100 128 86 17 41 3 247 224 3.411 .293 .204 .38 .432 4.916 80 305 .977 .59 100 2170 7630 30 40 80 90 0 166 118 47 .245 150 32 4.08 .171 -2.029 -2.55
6 2551 3127 75 152 2476 2975 2502 3308 92 186 2426 3156 0 0 513 723 58 181 100 100 100 100 5451 5582 .832 1.202 1.301 1.186 1.24 2.264 52 260 1.206 .95 90 2320 7630 30 39 95 104 0 2614 127 2487 1.004 2765 2638 .996 1.088 .006 .121
7 98 125 52 125 46 0 97 113 61 150 44 -11 0 0 35 72 29 154 62 1 33 1 46 33 null null null 1.075 1.124 9.073 80 346 10.188 .22 100 2470 7630 30 40 110 120 -50 104 104 0 null 94 -9 null null null null
8 6026 14182 49 115 5977 14067 6284 14461 53 136 6235 14346 0 0 1088 1986 21 88 100 100 100 100 20044 20581 .425 2.354 2.301 2.399 2.386 2.183 52 291 2.324 .96 90 2620 7630 30 39 125 134 0 11856 96 11760 1.967 12089 11993 .508 1.923 .976 .944
9 65 71 46 109 18 -38 61 63 51 133 15 -46 0 0 21 38 20 92 36 0 17 0 -20 -31 null null null 2.814 4.335 6.253 80 321 -1 -1 100 2770 7630 30 40 140 150 -50 59 91 -32 null 53 -38 null null null null
10 74 149 47 115 27 34 68 111 52 137 20 -3 0 0 37 191 23 108 46 6 17 5 61 17 .794 1.259 null 2.218 1.663 7.197 80 290 8.903 .48 100 2920 7620 29 39 155 165 -50 125 96 28 1.053 93 -3 .95 null .074 null
11 321 607 45 116 276 491 314 604 50 136 268 488 0 0 101 157 19 95 100 100 98 98 767 756 .562 1.779 1.821 1.863 1.822 2.711 52 239 1.79 .89 80 3070 7630 31 39 171 179 0 507 97 410 1.487 505 408 .672 1.522 .573 .606
12 185 349 45 112 139 236 182 349 49 128 136 236 0 0 49 105 18 80 100 92 100 76 375 372 .589 1.698 1.735 1.588 1.625 3.424 52 253 2.089 .73 80 3230 7630 31 39 187 195 0 292 94 197 1.419 292 197 .705 1.451 .505 .537
13 105 107 46 103 59 3 107 99 52 125 61 -3 0 0 51 42 21 82 70 5 57 0 62 58 19.667 .051 null .908 .719 8.031 80 365 2.389 .17 100 3380 7620 29 39 201 211 0 89 86 3 .043 83 -3 23.526 null -4.556 null
14 94 127 46 116 48 10 93 116 50 127 47 0 0 0 22 56 18 68 87 12 68 3 58 47 4.8 .208 null .967 .875 3.822 32 147 6.878 .17 60 3530 7630 32 38 218 224 0 106 97 8 .174 97 0 5.742 null -2.522 null
15 51 83 46 113 5 -30 49 64 48 128 3 -48 0 0 12 62 14 72 25 8 3 2 -25 -45 null null null 5.941 6.182 5.798 80 306 19.866 .29 100 3680 7630 30 40 231 241 -50 69 94 -25 null 54 -40 null null null null
16 255 635 45 121 210 513 281 641 47 132 235 520 0 0 71 161 14 59 100 98 100 98 723 755 .409 2.443 2.213 2.472 2.433 2.651 52 222 2.49 .88 90 3830 7630 30 39 246 255 0 531 101 429 2.042 536 435 .49 1.85 1.03 .887
17 69 101 45 112 24 -10 70 92 52 144 24 -19 0 0 21 62 49 149 16 2 0 1 14 5 null null null 2.139 2.502 5.13 80 289 3.292 .77 100 3980 7620 29 39 261 271 -50 84 94 -8 null 77 -16 null null null null
18 52 80 46 115 6 -34 48 54 54 148 1 -60 0 0 21 133 49 148 1 3 1 2 -28 -59 null null null 9.511 9.196 5.516 80 289 8.762 .76 100 4130 7620 29 39 276 286 -50 67 96 -28 null 45 -50 null null null null
19 136 162 47 120 89 42 134 153 49 144 86 33 0 0 42 63 15 124 100 7 92 0 131 119 2.119 .472 .384 .567 .707 5.161 52 245 .931 .36 80 4290 7620 30 38 293 301 0 135 100 35 .395 128 28 2.535 .321 -1.342 -1.64
20 846 4317 47 105 798 4211 837 4501 49 129 790 4395 0 0 130 926 17 87 100 100 100 100 5009 5185 .19 5.277 5.563 5.188 5.184 2.307 52 278 5.616 .95 90 4440 7620 29 38 307 316 0 3609 88 3520 4.411 3763 3674 .227 4.651 2.141 2.217

Total number of rows: 44544

Table truncated, full table size 9235 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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