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Sample GSM989750 Query DataSets for GSM989750
Status Public on Aug 23, 2012
Title PC 21T
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 21
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 61
pre-operation treatment: None
individual: PC 485T
disease free survival: 49.70
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/2008-11/81789.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 4163 3867 38 66 4125 3800 4606 4641 38 73 4568 4574 0 0 1444 1829 6 48 100 88 100 88 7925 9142 1.086 .921 1.001 .595 .948 10.098 52 321 .911 .83 80 1670 7020 30 38 47 55 0 3308 56 3251 .788 3970 3913 1.269 .857 -.344 -.223
2 3797 3079 41 71 3756 3008 4316 3805 45 95 4275 3734 0 0 1035 1775 16 125 100 88 100 86 6764 8009 1.249 .801 .873 .491 .891 6.727 52 321 .867 .85 90 1830 7020 29 38 62 71 0 2634 61 2573 .685 3255 3194 1.46 .747 -.546 -.42
3 6049 11434 42 72 6006 11362 6855 13826 45 79 6813 13754 0 0 1907 4741 14 48 100 100 100 100 17368 20567 .529 1.892 2.019 1.708 1.992 4.861 52 243 2.071 .86 80 1980 7030 31 39 78 86 0 9781 62 9720 1.618 11827 11766 .618 1.727 .694 .788
4 4559 3506 42 73 4517 3433 4842 4450 43 79 4800 4376 0 0 1160 1890 9 32 100 90 100 88 7950 9176 1.316 .76 .912 .498 .884 6.31 52 318 .822 .87 90 2130 7020 29 38 92 101 0 2999 62 2937 .65 3807 3743 1.538 .78 -.621 -.359
5 286 158 43 76 242 82 295 165 47 87 251 89 0 0 54 76 25 72 100 59 100 15 324 340 2.951 .339 .355 .342 .362 3.127 52 240 .523 .5 80 2280 7020 30 38 108 116 0 135 65 70 .29 141 76 3.45 .303 -1.787 -1.721
6 1575 2666 48 91 1526 2574 805 973 53 100 756 881 0 0 1467 2683 21 55 100 96 99 86 4100 1637 .593 1.687 1.165 1.481 1.741 4.006 120 566 1.808 .9 130 2430 7020 27 40 120 133 0 2281 78 2202 1.443 832 754 .693 .997 .529 -.004
7 100 118 43 87 57 31 97 116 45 91 54 29 0 0 19 41 9 43 100 31 96 12 88 83 1.839 .544 .537 .688 .929 4.774 32 154 2.541 .17 60 2590 7030 32 38 140 146 0 101 74 27 .465 99 25 2.149 .459 -1.104 -1.122
8 6580 13856 41 76 6539 13780 7980 17175 42 81 7939 17098 0 0 3022 6277 7 38 100 98 100 98 20319 25037 .475 2.107 2.154 1.891 2.099 7.364 52 269 2.209 .84 80 2730 7020 30 38 153 161 0 11853 65 11788 1.803 14692 14626 .555 1.842 .85 .882
9 82 74 45 72 37 2 83 74 52 73 38 2 0 0 18 32 19 30 91 25 50 0 39 40 18.5 .054 .053 .676 .975 4.166 12 68 -.668 -.36 40 2900 7000 30 34 172 176 0 63 62 2 .046 63 2 21.626 .045 -4.435 -4.473
10 119 95 39 77 79 18 121 91 40 79 81 14 0 0 15 30 5 26 100 37 100 18 97 95 4.389 .228 .173 .268 .357 4.594 32 193 .245 .22 70 3040 7020 30 37 184 191 0 81 66 15 .195 78 12 5.131 .148 -2.359 -2.758
11 339 790 38 73 301 717 353 824 39 78 314 750 0 0 110 293 5 31 98 98 96 98 1018 1064 .42 2.382 2.389 2.384 2.288 4.769 52 253 2.688 .82 80 3190 7020 30 38 199 207 0 676 62 613 2.038 705 642 .491 2.043 1.027 1.031
12 334 475 39 76 295 399 360 506 41 85 320 430 0 0 90 181 14 48 100 90 100 90 694 750 .739 1.353 1.344 1.447 1.403 3.415 52 246 1.46 .78 80 3340 7020 30 38 214 222 0 406 65 341 1.157 433 368 .864 1.15 .21 .201
13 174 145 39 77 134 67 191 141 40 82 152 64 0 0 59 54 13 39 96 69 88 44 201 216 2 .5 .421 .553 .507 4.222 52 264 .51 .57 80 3490 7020 30 38 229 237 0 124 66 57 .428 121 55 2.338 .36 -1.225 -1.473
14 107 166 38 74 68 91 116 171 39 79 77 96 0 0 32 67 5 32 92 75 88 67 159 173 .747 1.338 1.247 1.104 1.294 4.09 52 257 4.303 .43 80 3650 7020 30 38 245 253 0 142 63 78 1.145 146 82 .874 1.067 .195 .093
15 38 55 39 79 0 -24 38 48 40 87 0 -31 0 0 4 27 6 39 10 3 1 0 -24 -31 null null null 10.636 10.48 3.414 80 339 62.536 .09 100 3800 7020 29 39 259 269 -50 47 68 -21 null 41 -27 null null null null
16 731 1394 40 83 690 1310 774 1544 41 87 734 1460 0 0 176 562 6 31 100 98 100 98 2000 2194 .527 1.899 1.989 1.579 2.001 4.169 52 250 2.24 .82 80 3950 7020 30 38 275 283 0 1192 71 1121 1.624 1321 1249 .616 1.702 .7 .767
17 106 82 42 84 64 -2 105 78 43 88 63 -6 0 0 15 31 7 32 100 15 100 0 62 57 null null null .365 .431 4.027 32 194 -.232 -.08 70 4110 7010 29 36 291 298 0 70 72 -2 null 67 -5 null null null null
18 43 64 46 97 -3 -33 41 58 47 102 -4 -39 0 0 8 32 9 36 5 5 0 0 -36 -43 null null null 6.107 5.624 3.202 80 380 19.693 .2 100 4250 7010 28 38 304 314 -50 55 83 -28 null 50 -33 null null null null
19 224 399 53 122 170 276 234 385 54 134 180 263 0 0 68 90 12 77 94 100 92 94 446 443 .616 1.624 1.461 1.832 1.456 3.57 52 306 1.525 .71 90 4400 7020 29 38 319 328 0 341 104 236 1.389 329 225 .72 1.25 .474 .322
20 885 6370 53 137 831 6232 998 6841 56 159 944 6704 0 0 366 1553 14 141 90 100 90 100 7063 7648 .133 7.499 7.102 9.908 6.964 4.496 52 267 7.589 .87 90 4550 7020 29 38 334 343 0 5449 117 5331 6.415 5852 5735 .156 6.075 2.682 2.603

Total number of rows: 44544

Table truncated, full table size 9313 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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