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Sample GSM989781 Query DataSets for GSM989781
Status Public on Aug 23, 2012
Title PC 343N
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 343N2
Organism Homo sapiens
Characteristics individual: PC 343N
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/2008-08/81115.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 37 35 36 27 0 7 35 23 38 39 0 -4 0 0 5 21 4 25 15 21 5 5 7 -4 null null null 4.57 5.592 2.762 52 387 57.467 .08 90 1990 7220 25 34 46 55 -50 29 23 6 null 19 -3 null null null null
2 37 35 36 30 0 5 36 25 37 39 0 -4 0 0 3 21 4 23 13 17 1 7 5 -4 null null null 4.852 3.728 4.196 52 320 115.209 .04 90 2150 7220 25 34 62 71 -50 29 25 4 null 21 -3 null null null null
3 38 37 36 31 1 6 36 30 38 39 0 -1 0 0 5 23 5 21 15 19 5 11 7 -1 .167 6 null 4.149 3.947 4.069 52 310 109.833 .03 90 2300 7220 25 34 77 86 -50 31 26 5 5.033 25 -1 .199 null 2.332 null
4 37 34 36 25 0 8 37 27 38 34 0 2 0 0 4 21 5 22 11 21 1 5 8 2 null null null 3.629 3.198 3.938 52 310 97.091 .04 90 2450 7220 25 34 92 101 -50 29 21 7 null 23 2 null null null null
5 38 42 36 30 1 12 36 33 38 40 0 3 0 0 4 23 5 25 15 23 5 7 13 3 .083 12 null 3.012 2.485 4.98 52 310 -93.265 -.05 90 2600 7220 25 34 107 116 -50 35 25 10 10.067 28 3 .099 null 3.332 null
6 38 45 36 30 1 15 36 35 37 37 0 5 0 0 6 27 4 23 17 26 9 15 16 5 .067 15 null 3.489 3.572 4.563 52 315 181.52 .03 90 2750 7220 25 34 122 131 -50 38 25 13 12.584 29 4 .079 null 3.653 null
7 38 34 36 26 1 7 35 22 38 35 0 -4 0 0 6 24 4 24 19 19 13 5 8 -4 .143 7 null 2.414 2.889 3.664 52 311 -83.819 -.05 90 2900 7220 25 34 137 146 -50 29 22 6 5.872 18 -3 .17 null 2.554 null
8 38 49 36 33 1 15 36 45 38 41 0 12 0 0 5 26 4 22 21 28 11 9 16 12 .067 15 null 4.571 4.453 2.904 52 321 53.561 .08 90 3050 7220 25 34 152 161 -50 41 28 13 12.584 38 10 .079 null 3.653 null
9 38 44 36 28 1 15 37 36 38 39 0 7 0 0 3 27 5 24 17 25 0 11 16 7 .067 15 null 5.608 5.108 3.981 52 306 76.621 .06 90 3210 7220 25 34 168 177 -50 37 23 13 12.584 30 6 .079 null 3.653 null
10 39 39 37 27 1 11 38 27 38 35 0 0 0 0 4 22 5 22 15 23 5 9 12 0 .091 11 null 4.01 4.97 5.415 52 294 -58.418 -.07 90 3360 7220 25 34 183 192 -50 33 23 9 9.228 23 0 .108 null 3.206 null
11 38 36 36 32 1 4 36 28 38 42 0 -3 0 0 4 18 4 24 19 11 11 3 5 -3 .25 4 null 5.199 6.213 3.271 52 302 -1 -1 90 3510 7220 25 34 198 207 -50 30 27 3 3.356 23 -3 .298 null 1.747 null
12 40 36 36 27 3 8 37 26 38 37 0 -1 0 0 5 25 5 33 26 11 15 5 11 -1 .375 2.667 null 2.766 3.106 4.155 52 292 231.625 .03 90 3660 7220 25 34 213 222 -50 30 23 7 2.237 22 -1 .447 null 1.162 null
13 38 47 36 33 1 14 36 32 38 42 0 -1 0 0 5 30 5 33 15 26 7 5 15 -1 .071 14 null 7.23 6.213 4.19 52 298 -81.415 -.05 90 3810 7220 25 34 228 237 -50 39 28 12 11.745 27 -1 .085 null 3.554 null
14 38 45 36 33 1 12 36 37 37 44 0 4 0 0 4 25 4 25 17 25 7 11 13 4 .083 12 null 6.283 6.627 2.943 52 312 166.846 .03 90 3960 7220 25 34 243 252 -50 38 28 10 10.067 31 3 .099 null 3.332 null
15 38 34 36 30 1 4 37 25 37 40 0 -4 0 0 4 20 4 26 25 15 5 1 5 -4 .25 4 null 3.371 3.728 3.045 52 346 -67.867 -.08 90 4110 7220 25 34 258 267 -50 29 25 3 3.356 21 -3 .298 null 1.747 null
16 38 50 35 26 2 23 36 45 37 36 0 18 0 0 3 27 4 22 25 50 8 8 25 18 .087 11.5 null 3.986 3.705 4.382 12 68 108.517 .06 40 4270 7220 28 32 277 281 0 42 22 19 9.647 38 15 .104 null 3.27 null
17 38 43 36 33 1 10 37 32 38 44 0 -1 0 0 4 25 4 27 15 15 9 6 11 -1 .1 10 null 4.12 5.902 5.714 32 173 -63.971 -.08 60 4420 7220 27 33 291 297 0 36 28 8 8.389 27 -1 .119 null 3.069 null
18 40 35 36 28 3 6 38 27 38 37 1 -1 0 0 6 21 4 22 28 21 15 9 9 0 .5 2 null 2.094 2.028 4.773 52 323 -72.306 -.04 90 4570 7210 24 33 304 313 -50 29 23 5 1.678 23 -1 .596 null .747 null
19 39 42 36 33 2 8 38 33 38 42 1 0 0 0 5 23 5 25 21 21 11 5 10 1 .25 4 null 4.076 4.014 5.462 52 310 -1 -1 90 4720 7210 24 33 319 328 -50 35 28 7 3.356 28 0 .298 null 1.747 null
20 37 32 36 30 0 2 36 26 38 39 0 -3 0 0 4 16 5 25 13 11 3 1 2 -3 null null null 3.376 2.485 3.947 52 315 -1 -1 90 4870 7210 24 33 334 343 -50 27 25 2 null 22 -3 null null null null

Total number of rows: 44544

Table truncated, full table size 9505 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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