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Sample GSM989762 Query DataSets for GSM989762
Status Public on Aug 23, 2012
Title PC 555T
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 555T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 59
pre-operation treatment: None
individual: PC 616T
disease free survival: 1.37
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/2008-08/81085.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 5398 4207 92 149 5306 4057 6452 4843 96 169 6360 4693 0 0 2901 1718 33 93 100 100 100 100 9363 11053 1.308 .765 .738 .906 .748 2.97 32 176 .683 .94 60 2030 6860 23 29 60 66 0 3477 123 3353 .632 4003 3879 1.582 .61 -.662 -.713
2 5148 3631 89 139 5059 3492 6097 4511 94 158 6008 4371 0 0 3933 1989 36 113 96 100 93 93 8551 10379 1.449 .69 .728 1.199 .744 4.986 32 168 .578 .93 60 2180 6860 23 29 75 81 0 3001 115 2886 .57 3728 3612 1.753 .601 -.81 -.734
3 2492 4711 82 148 2409 4563 2676 4599 86 171 2593 4451 0 0 796 783 27 107 100 100 100 100 6972 7044 .528 1.894 1.717 2.005 1.807 2.384 12 104 1.782 .92 50 2330 6850 22 27 90 95 0 3893 122 3771 1.565 3801 3679 .639 1.419 .647 .505
4 6868 4830 86 141 6781 4688 8717 5556 89 163 8631 5414 0 0 3829 1960 29 99 100 96 100 96 11469 14045 1.446 .691 .627 .738 .644 3.575 32 173 .608 .94 60 2480 6850 22 28 105 111 0 3992 117 3874 .571 4592 4474 1.75 .518 -.808 -.948
5 254 162 82 126 172 35 248 140 82 143 165 14 0 0 71 75 25 77 100 25 91 8 207 179 4.914 .203 .085 .27 .233 7.306 12 68 .125 .06 40 2630 6860 24 28 121 125 0 134 104 29 .168 116 12 5.946 .07 -2.572 -3.834
6 2783 2115 87 148 2695 1966 3192 2182 92 161 3104 2034 0 0 906 442 32 85 100 100 100 100 4661 5138 1.371 .729 .655 .794 .715 2.633 32 222 .674 .93 70 2780 6860 22 29 134 141 0 1748 122 1625 .603 1803 1681 1.659 .542 -.73 -.885
7 109 123 77 153 32 -29 94 116 81 169 17 -37 0 0 39 58 27 95 42 7 28 0 3 -20 null null null 3.294 3.72 9.445 52 317 -28.973 -.06 90 2930 6850 20 29 148 157 -50 102 126 -24 null 96 -31 null null null null
8 1445 2789 74 145 1370 2644 444 1593 79 172 370 1447 0 0 1589 2811 25 173 71 51 57 51 4014 1817 .518 1.93 3.911 2.338 1.844 3.914 52 291 1.869 .93 90 3080 6850 20 29 163 172 -50 2305 120 2185 1.595 1317 1196 .627 3.232 .674 1.692
9 93 161 71 125 21 35 93 144 75 138 21 19 0 0 22 79 23 79 48 25 9 9 56 40 .6 1.667 .905 3.095 4.2 8.168 52 291 -1 -1 90 3230 6850 20 29 178 187 -50 133 103 29 1.377 119 16 .726 .748 .462 -.419
10 96 139 77 120 18 19 100 121 79 141 22 1 0 0 26 81 24 80 46 25 13 3 37 23 .947 1.056 .045 2.89 2.46 5.448 52 302 55.804 .03 90 3380 6850 20 29 193 202 -50 115 99 16 .872 100 1 1.146 .038 -.197 -4.734
11 225 378 83 127 141 250 210 374 87 150 126 246 0 0 62 134 28 94 100 87 96 62 391 372 .564 1.773 1.952 1.61 1.834 3.56 32 158 2.295 .54 60 3540 6860 23 29 211 217 0 312 105 207 1.465 309 203 .682 1.614 .551 .69
12 154 250 77 125 76 125 154 227 79 141 76 102 0 0 39 111 23 77 87 62 75 31 201 178 .608 1.645 1.342 1.773 1.416 4.777 32 208 1.311 .5 70 3690 6860 22 29 225 232 0 207 103 103 1.359 188 84 .736 1.109 .443 .15
13 133 163 81 134 52 29 123 140 86 158 42 6 0 0 50 89 25 100 67 19 38 3 81 48 1.793 .558 .143 2.433 2.359 5.359 52 301 13.91 .14 90 3830 6850 20 29 238 247 -50 135 111 24 .461 116 5 2.17 .118 -1.117 -3.082
14 109 157 79 131 29 25 111 135 81 154 31 3 0 0 34 102 28 116 50 13 19 3 54 34 1.16 .862 .097 1.73 2.303 7.758 52 272 22.899 .12 90 3980 6850 20 29 253 262 -50 130 108 21 .712 112 2 1.404 .08 -.489 -3.644
15 98 122 75 130 22 -7 93 102 78 148 17 -28 0 0 31 77 25 85 38 9 19 5 15 -11 null null null 2.703 3.344 9.445 52 292 47.269 .09 90 4130 6850 20 29 268 277 -50 101 107 -6 null 84 -23 null null null null
16 461 304 77 152 384 152 507 274 84 169 429 122 0 0 195 108 29 97 93 68 93 34 536 551 2.526 .396 .284 .391 .432 3.374 32 162 .371 .54 60 4290 6850 22 28 286 292 0 251 126 126 .327 226 101 3.057 .235 -1.612 -2.089
17 109 149 74 134 35 15 111 141 77 144 37 7 0 0 39 60 24 74 65 17 32 1 50 44 2.333 .429 .189 .88 1.005 6.542 52 276 7.56 .17 90 4430 6850 20 29 298 307 -50 123 111 12 .354 117 6 2.823 .156 -1.497 -2.677
18 96 125 73 129 22 -3 86 115 76 146 12 -14 0 0 37 62 25 98 34 7 17 0 19 -2 null null null 1.626 1.739 6.996 52 292 14.314 .12 90 4580 6850 20 29 313 322 -50 103 107 -2 null 95 -12 null null null null
19 179 194 73 107 105 86 187 171 75 125 114 63 0 0 79 134 23 76 87 37 78 21 191 177 1.221 .819 .553 .8 1.024 6.566 32 231 1.178 .15 70 4740 6850 21 28 330 337 0 160 88 71 .677 141 52 1.477 .457 -.563 -1.131
20 498 889 72 100 425 788 490 861 73 118 417 760 0 0 149 295 18 80 100 100 100 100 1213 1177 .539 1.854 1.823 1.837 1.93 2.819 12 68 2.065 .76 40 4880 6850 23 27 346 350 0 735 83 651 1.532 712 628 .653 1.506 .616 .591

Total number of rows: 44544

Table truncated, full table size 9379 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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