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Sample GSM989791 Query DataSets for GSM989791
Status Public on Aug 23, 2012
Title PC 19T2
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 19T2.0
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 57
pre-operation treatment: None
individual: PC 19T
disease free survival: 19.13
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/2008-08/81244.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 GPL15971
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 44702 17489 63 47 44638 17442 54043 19835 98 73 53979 19787 67 0 16875 6212 150 65 100 100 100 100 62080 73766 2.559 .391 .367 .412 .392 2.438 80 418 .376 .97 100 1750 6670 26 36 30 40 -100 16418 44 16373 .367 18620 18575 2.726 .344 -1.447 -1.539
2 40707 17550 65 49 40641 17500 54043 22384 87 70 53978 22334 61 0 19885 9721 91 58 100 98 100 97 58141 76312 2.322 .431 .414 .38 .443 4.213 80 375 .423 .94 100 1890 6630 22 32 44 54 -100 16475 46 16428 .404 21013 20966 2.474 .388 -1.307 -1.364
3 41838 29394 78 61 41760 29332 42765 30628 111 106 42687 30567 0 0 6187 6583 107 253 100 100 100 100 71092 73254 1.424 .702 .716 .665 .705 2.321 52 317 .702 .94 90 2060 6640 23 32 61 70 0 27593 57 27535 .659 28752 28694 1.517 .672 -.601 -.573
4 50639 23168 59 59 50580 23109 54043 24916 98 106 53983 24856 85 0 9870 5869 103 237 100 100 100 100 73689 78839 2.189 .457 .46 .444 .469 2.269 80 373 .451 .96 110 2210 6660 24 35 75 86 -100 21749 55 21693 .429 23390 23333 2.332 .432 -1.221 -1.21
5 2359 545 52 53 2306 492 2532 552 63 70 2479 499 0 0 640 192 61 50 98 97 98 96 2798 2978 4.687 .213 .201 .207 .207 3.177 80 358 .196 .87 110 2360 6660 24 35 90 101 0 512 50 462 .2 518 468 4.993 .189 -2.32 -2.404
6 18377 20487 69 55 18307 20431 20329 23206 117 76 20259 23150 0 0 8732 9567 144 60 100 100 99 99 38738 43409 .896 1.116 1.143 1.124 1.106 2.834 120 420 1.108 .97 120 2510 6660 24 36 105 117 0 19232 52 19179 1.048 21784 21732 .955 1.073 .067 .101
7 667 260 121 70 546 190 673 259 218 187 552 189 0 0 105 104 699 916 5 0 0 0 736 741 2.874 .348 .342 .288 .349 3.31 52 255 1.059 .38 90 2670 6650 24 33 122 131 0 244 66 178 .327 243 177 3.061 .321 -1.614 -1.637
8 44889 30503 84 73 44805 30430 45559 31602 308 346 45475 31528 0 0 4349 4479 1991 1895 100 100 100 100 75235 77003 1.472 .679 .693 .671 .687 1.782 52 291 .679 .96 90 2810 6640 23 32 136 145 0 28634 69 28566 .638 29666 29596 1.568 .651 -.649 -.62
9 286 276 57 53 229 223 288 258 191 207 230 204 0 0 89 126 1674 1506 0 0 0 0 452 434 1.027 .974 .887 .883 .959 3.884 80 372 .886 .97 110 2960 6660 24 35 150 161 0 259 50 209 .914 242 192 1.094 .833 -.13 -.264
10 284 167 54 48 230 118 282 167 58 61 227 118 0 0 63 89 17 42 100 73 98 58 348 345 1.949 .513 .52 .382 .557 4.746 80 344 .489 .59 100 3110 6660 25 35 166 176 0 157 45 111 .482 157 111 2.076 .488 -1.054 -1.035
11 978 805 51 48 926 756 1064 877 54 61 1013 829 0 0 534 438 15 47 94 91 90 86 1682 1842 1.225 .816 .818 .88 .805 3.866 120 408 .78 .92 120 3260 6660 24 36 180 192 0 756 45 710 .766 823 778 1.305 .768 -.384 -.38
12 680 890 48 47 631 842 752 960 51 59 703 913 0 0 330 457 12 38 96 96 92 91 1473 1616 .749 1.334 1.299 1.359 1.361 4.098 120 339 1.335 .89 120 3410 6660 24 36 195 207 0 835 44 790 1.253 901 857 .798 1.219 .325 .286
13 628 210 47 47 580 163 651 196 51 60 603 149 0 0 191 94 13 41 97 90 97 83 743 752 3.558 .281 .247 .261 .27 2.843 80 279 .248 .66 110 3560 6650 23 34 210 221 0 197 44 153 .264 184 140 3.791 .232 -1.922 -2.108
14 200 270 47 49 152 220 203 246 50 66 155 196 0 0 76 140 12 47 95 90 92 79 372 351 .691 1.447 1.265 1.427 1.515 3.647 120 314 1.673 .73 120 3710 6650 23 35 225 237 0 253 46 207 1.359 231 184 .736 1.187 .442 .247
15 56 59 49 49 6 9 53 43 51 66 4 -6 0 0 13 42 12 49 28 14 8 5 15 -2 .667 1.5 null 3.323 3.382 3.522 120 353 -1 -1 120 3860 6640 22 34 240 252 -50 55 46 8 1.408 40 -6 .71 null .494 null
16 1402 669 51 46 1351 623 1473 692 53 63 1422 646 0 0 451 264 13 54 100 97 100 93 1974 2068 2.169 .461 .454 .428 .447 3.634 80 386 .435 .87 110 4020 6640 22 33 256 267 0 628 43 585 .433 650 606 2.31 .426 -1.208 -1.23
17 150 237 51 48 98 189 153 223 55 63 102 174 0 0 47 124 14 43 95 91 92 78 287 276 .519 1.929 1.706 1.611 1.758 4.223 80 262 2.635 .59 100 4170 6650 24 34 272 282 0 222 45 177 1.81 209 163 .552 1.601 .856 .679
18 56 59 51 44 4 14 52 44 55 59 1 0 0 0 14 46 16 41 15 22 6 5 18 1 .286 3.5 null 2.274 2.144 5.831 120 302 50.465 .05 120 4320 6650 23 35 286 298 -50 55 41 13 3.286 41 0 .304 null 1.716 null
19 775 514 53 49 722 464 787 514 57 67 733 464 0 0 384 305 18 64 96 92 94 88 1186 1197 1.556 .643 .633 .676 .618 4.1 120 310 .567 .74 120 4470 6650 23 35 301 313 0 483 46 436 .603 483 436 1.658 .594 -.729 -.751
20 3440 5867 54 50 3385 5817 3837 6767 57 66 3782 6716 0 0 1609 2831 16 60 100 95 98 94 9202 10498 .582 1.718 1.776 1.612 1.734 3.76 120 420 1.738 .95 120 4620 6650 23 35 316 328 0 5508 47 5461 1.613 6352 6305 .62 1.667 .69 .737

Total number of rows: 44544

Table truncated, full table size 9358 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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