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Sample GSM989796 Query DataSets for GSM989796
Status Public on Aug 23, 2012
Title PC 393N
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 393N2
Organism Homo sapiens
Characteristics individual: PC 393N
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/2008-08/81243.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 5826 4890 49 72 5776 4818 6397 5344 52 90 6347 5272 0 0 2825 2576 16 63 98 95 97 93 10594 11619 1.199 .834 .831 .916 .784 15.949 80 519 .725 .81 110 1770 6950 53 64 31 42 0 4879 72 4808 .832 5332 5261 1.201 .829 -.265 -.271
2 5326 3765 56 76 5269 3688 5372 4155 63 95 5315 4078 0 0 1434 1767 30 69 100 96 100 92 8957 9393 1.429 .7 .767 .492 .729 8.19 52 325 .713 .81 90 1910 6930 52 61 46 55 0 3757 76 3680 .698 4146 4069 1.432 .766 -.518 -.385
3 8280 4689 57 75 8222 4614 8914 5129 62 93 8856 5053 0 0 3624 2513 29 69 100 98 100 95 12836 13909 1.782 .561 .571 .509 .566 7.672 80 352 .503 .82 110 2090 6960 54 65 63 74 0 4679 75 4604 .56 5118 5042 1.786 .569 -.837 -.813
4 4290 3408 51 58 4239 3349 4494 3535 53 84 4442 3477 0 0 1848 1708 16 63 100 96 100 95 7588 7919 1.266 .79 .783 .706 .713 11.182 80 293 .656 .77 110 2230 6960 54 65 77 88 0 3401 58 3342 .788 3527 3469 1.268 .781 -.343 -.356
5 404 146 53 69 351 76 402 130 58 90 349 61 0 0 79 86 27 66 100 48 100 23 427 410 4.618 .217 .175 .222 .199 6.84 52 251 .104 .16 80 2370 6930 53 61 93 101 0 146 69 76 .216 130 61 4.628 .174 -2.211 -2.519
6 2990 2688 58 81 2932 2606 2866 2699 67 99 2807 2617 0 0 729 1062 35 84 100 98 100 96 5538 5424 1.125 .889 .932 .807 .938 4.691 80 392 .875 .85 110 2530 6950 53 64 107 118 0 2682 81 2600 .887 2693 2611 1.128 .93 -.173 -.104
7 153 132 57 86 95 46 146 118 64 112 89 32 0 0 48 87 27 121 98 15 78 3 141 121 2.065 .484 .36 .779 .765 7.618 52 208 -1 -1 80 2680 6960 56 64 124 132 0 132 86 46 .483 118 32 2.07 .359 -1.049 -1.479
8 5778 3148 51 76 5726 3071 6126 3337 54 93 6074 3260 0 0 2285 1531 18 61 100 93 97 91 8797 9334 1.865 .536 .537 .557 .551 9.35 80 386 .495 .83 110 2830 6940 52 63 137 148 0 3141 76 3064 .535 3330 3253 1.869 .536 -.902 -.901
9 108 132 55 86 53 46 108 96 63 107 53 10 0 0 26 99 27 75 78 34 43 15 99 63 1.152 .868 .189 1.049 1.307 16.06 32 141 -1.94 -.09 70 2970 6960 56 63 153 160 0 132 86 46 .866 96 10 1.155 .188 -.207 -2.409
10 122 146 50 70 72 75 122 132 53 90 72 61 0 0 43 95 20 66 88 45 76 18 147 133 .96 1.042 .847 1.168 1.194 7.647 80 316 1.909 .26 100 3130 6950 54 64 168 178 0 146 70 75 1.039 132 61 .962 .845 .056 -.242
11 216 266 50 83 165 183 209 253 52 98 158 170 0 0 90 155 18 67 93 72 90 60 348 328 .902 1.109 1.076 1.046 1.074 8.254 80 261 .967 .49 100 3280 6950 54 64 183 193 0 265 83 183 1.107 252 170 .904 1.074 .146 .102
12 194 570 52 75 142 495 193 521 55 95 141 446 0 0 78 284 19 75 91 95 91 88 637 587 .287 3.486 3.163 3.178 3.189 5.436 80 353 4.144 .68 110 3430 6950 53 64 197 208 0 569 75 494 3.478 520 445 .287 3.156 1.798 1.658
13 166 118 49 78 117 39 160 107 52 99 111 29 0 0 54 78 18 76 96 23 93 6 156 140 3 .333 .261 .473 .504 7.418 80 307 .252 .14 100 3590 6950 54 64 214 224 0 118 78 39 .333 107 29 3.006 .261 -1.588 -1.94
14 126 139 47 79 79 59 128 112 50 95 80 32 0 0 30 96 14 70 98 40 97 16 138 112 1.339 .747 .4 1.001 1.182 7.098 80 224 .911 .2 100 3730 6950 54 64 228 238 0 139 79 59 .745 112 32 1.342 .399 -.424 -1.325
15 66 90 49 64 16 26 59 69 53 95 10 4 0 0 25 66 18 70 40 18 20 5 42 14 .615 1.625 .4 1.858 2.136 12.588 120 408 -21.508 -.08 120 3880 6940 52 64 242 254 -50 90 64 26 1.621 69 4 .617 .399 .697 -1.325
16 557 355 50 72 507 282 581 353 53 93 531 281 0 0 197 201 16 67 98 85 97 72 789 812 1.798 .556 .529 .495 .484 7.276 80 262 .434 .59 100 4040 6940 53 63 259 269 0 354 72 281 .555 352 280 1.802 .528 -.849 -.921
17 90 116 48 64 41 52 88 106 52 83 39 41 0 0 27 70 16 59 72 30 60 13 93 80 .788 1.268 1.051 1.592 1.466 8.953 80 320 4.7 .11 110 4200 6930 51 62 274 285 0 116 64 52 1.266 106 41 .79 1.049 .34 .069
18 59 103 60 50 0 52 58 86 63 78 -1 35 0 0 17 70 20 56 15 43 0 18 52 34 null null null 4.672 5.437 8.627 32 72 -36.113 -.03 60 4310 6970 58 64 288 294 0 103 50 52 null 86 35 null null null null
19 191 155 51 78 140 76 187 143 55 104 135 64 0 0 58 96 21 104 100 33 98 8 216 199 1.842 .543 .474 .58 .644 6.596 80 290 .374 .25 100 4500 6950 54 64 305 315 0 155 78 76 .542 143 64 1.846 .473 -.884 -1.08
20 728 1651 51 76 676 1574 724 1614 61 129 673 1538 0 0 287 659 55 262 91 97 91 92 2250 2211 .429 2.328 2.285 2.751 2.326 8.325 80 240 2.337 .77 100 4650 6940 53 63 320 330 0 1647 76 1571 2.323 1611 1535 .43 2.28 1.216 1.189

Total number of rows: 44544

Table truncated, full table size 9583 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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