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Sample GSM989826 Query DataSets for GSM989826
Status Public on Aug 23, 2012
Title PC 88N
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 88N2
Organism Homo sapiens
Characteristics individual: PC 88N
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/2008-08/81111.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) [email protected]
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 7855 6916 67 99 7787 6817 9072 7577 76 117 9005 7477 0 0 3046 2011 31 78 100 100 100 100 14604 16482 1.142 .875 .83 .948 .876 1.947 32 236 .827 .95 70 1730 7110 35 42 21 28 0 5658 81 5577 .716 6199 6117 1.396 .679 -.481 -.558
2 8073 6312 80 114 7992 6197 9542 7844 84 123 9462 7729 0 0 2950 3228 25 66 100 100 100 96 14189 17191 1.29 .775 .817 .586 .834 3.081 32 176 .811 .93 60 1890 7100 35 41 38 44 0 5164 93 5070 .634 6418 6324 1.576 .668 -.657 -.581
3 11835 8572 95 120 11739 8452 14051 10144 96 125 13955 10024 0 0 4412 3495 28 49 100 100 100 100 20191 23979 1.389 .72 .718 .683 .741 2.055 32 176 .713 .95 60 2040 7100 35 41 53 59 0 7013 98 6915 .589 8300 8201 1.698 .588 -.763 -.767
4 8950 7398 72 104 8877 7294 9417 7678 80 117 9344 7574 0 0 1875 1331 26 70 100 100 100 100 16171 16918 1.217 .822 .811 .831 .797 1.487 32 223 .797 .95 70 2190 7110 35 42 67 74 0 6053 85 5968 .672 6282 6197 1.488 .663 -.573 -.593
5 585 119 69 94 515 24 598 128 73 103 528 34 0 0 153 56 22 49 100 31 100 6 539 562 21.458 .047 .064 .091 .091 2.848 32 171 .029 .09 60 2340 7100 35 41 83 89 0 97 77 20 .038 105 28 26.227 .053 -4.713 -4.246
6 8700 5300 114 132 8586 5167 8640 5345 121 142 8525 5212 0 0 1296 951 53 69 100 100 100 100 13753 13737 1.662 .602 .611 .596 .623 1.454 32 221 .594 .96 70 2490 7100 34 41 97 104 0 4336 108 4227 .492 4373 4264 2.031 .5 -1.022 -.999
7 164 82 76 103 88 -20 160 75 83 118 83 -27 0 0 62 32 37 70 69 1 61 0 68 56 null null null .353 .27 8.163 52 342 -1.474 -.08 90 2640 7100 33 42 111 120 -50 67 84 -16 null 61 -22 null null null null
8 12992 10045 69 98 12922 9946 14630 11279 78 130 14560 11180 0 0 4421 3068 79 210 100 100 100 100 22868 25740 1.299 .77 .768 .812 .797 1.566 32 215 .752 .98 70 2790 7100 34 41 127 134 0 8219 80 8138 .63 9228 9147 1.588 .628 -.667 -.671
9 93 91 67 90 26 1 91 83 69 99 24 -6 0 0 25 42 19 48 53 11 28 3 27 18 26 .038 null 1.645 1.379 5.618 52 284 8.508 .22 90 2940 7100 33 42 141 150 -50 74 74 1 .031 68 -5 31.778 null -4.99 null
10 93 107 64 85 28 21 94 100 67 98 29 15 0 0 30 45 20 55 53 21 32 3 49 44 1.333 .75 .517 1.014 1.168 4.747 52 293 11.194 .14 90 3090 7100 33 42 156 165 -50 88 70 17 .614 82 12 1.63 .423 -.705 -1.241
11 454 466 63 88 390 378 467 503 68 103 403 415 0 0 92 172 25 63 100 93 100 87 768 818 1.032 .969 1.03 .851 1.013 2.392 32 233 1.145 .87 70 3250 7090 33 40 173 180 0 381 72 309 .793 412 340 1.261 .843 -.335 -.247
12 251 334 63 89 188 244 246 336 68 104 183 247 0 0 43 98 27 62 100 100 100 90 432 430 .77 1.298 1.35 1.234 1.33 1.808 32 171 1.657 .76 60 3400 7100 35 41 189 195 0 273 73 200 1.062 275 202 .942 1.104 .087 .143
13 202 125 66 93 136 32 202 123 113 146 136 30 0 0 41 49 379 373 0 0 0 0 168 166 4.25 .235 .221 .296 .348 3.429 32 214 .315 .74 70 3550 7100 34 41 203 210 0 102 76 26 .193 101 25 5.195 .18 -2.377 -2.47
14 167 94 62 89 105 5 173 94 87 104 110 5 0 0 41 38 312 79 0 6 0 0 110 115 21 .048 .045 .269 .296 4.199 32 209 -1 -1 70 3700 7100 34 41 218 225 0 77 73 4 .039 77 4 25.667 .037 -4.682 -4.749
15 70 62 60 82 10 -20 69 51 65 91 9 -31 0 0 14 33 17 49 32 3 3 0 -10 -22 null null null 3.109 3.108 3.748 52 341 10.923 .19 90 3850 7090 32 41 232 241 -50 51 67 -16 null 42 -25 null null null null
16 1643 506 63 83 1580 422 1698 525 67 90 1635 441 0 0 237 111 17 50 100 100 100 100 2002 2076 3.744 .267 .27 .259 .275 1.625 32 175 .256 .91 60 4000 7090 34 40 249 255 0 414 68 345 .219 430 361 4.576 .221 -2.194 -2.18
17 80 78 66 90 14 -11 77 73 73 116 11 -17 0 0 23 33 41 97 11 0 0 0 3 -6 null null null 1.821 1.376 5.551 52 308 5.93 .29 90 4150 7090 32 41 262 271 -50 64 74 -9 null 60 -14 null null null null
18 74 70 66 96 8 -25 71 54 71 111 5 -41 0 0 15 64 31 74 5 5 0 3 -17 -36 null null null 4.666 5.675 6.33 52 303 2.06 .47 90 4300 7090 32 41 277 286 -50 57 79 -20 null 44 -34 null null null null
19 342 136 64 92 278 44 340 132 70 105 276 39 0 0 55 50 40 73 100 18 100 3 322 315 6.318 .158 .141 .166 .196 2.661 32 224 .169 .35 70 4450 7090 33 40 293 300 0 111 75 36 .129 108 32 7.722 .116 -2.949 -3.113
20 1299 1875 64 95 1235 1780 1409 2008 67 106 1344 1912 0 0 409 464 23 61 100 100 100 100 3015 3256 .694 1.441 1.423 1.561 1.429 1.749 32 174 1.417 .97 60 4600 7100 35 41 309 315 0 1534 78 1456 1.179 1643 1564 .848 1.164 .238 .219

Total number of rows: 44544

Table truncated, full table size 9347 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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