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Sample GSM989803 Query DataSets for GSM989803
Status Public on Aug 23, 2012
Title PC 636N
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 636N2
Organism Homo sapiens
Characteristics individual: PC 636N
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/2008-08/81155.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 10067 8087 176 177 9890 7910 10268 8210 184 187 10092 8033 0 0 1401 1235 62 60 100 100 100 100 17800 18125 1.25 .8 .796 .797 .797 1.108 32 236 .797 .98 70 2000 6830 39 46 56 63 0 7565 166 7400 .748 7680 7515 1.337 .745 -.419 -.425
2 11939 9638 179 177 11759 9461 12374 9800 213 185 12194 9622 0 0 2020 1531 255 68 100 100 100 100 21220 21816 1.243 .805 .789 .807 .82 1.104 32 223 .818 .97 70 2160 6830 39 46 72 79 0 9016 166 8851 .753 9168 9001 1.329 .738 -.41 -.438
3 14582 12983 178 178 14403 12804 15584 13384 186 186 15405 13206 0 0 3734 3090 61 64 100 100 100 100 27207 28611 1.125 .889 .857 .902 .885 1.131 32 229 .883 .98 70 2300 6830 39 46 86 93 0 12145 167 11978 .832 12520 12354 1.202 .802 -.266 -.318
4 12887 10517 186 192 12700 10325 14037 12002 192 194 13851 11810 0 0 4569 4413 58 60 100 98 100 98 23025 25661 1.23 .813 .853 .738 .843 1.542 52 304 .84 .97 90 2460 6850 40 49 101 110 0 9838 180 9659 .761 11228 11048 1.315 .798 -.395 -.326
5 979 221 179 190 800 31 973 213 188 195 794 23 0 0 151 59 64 53 100 28 100 12 831 817 25.806 .039 .029 .061 .058 2.319 32 204 .046 .25 70 2610 6840 40 47 117 124 0 207 178 29 .036 199 22 27.587 .027 -4.786 -5.206
6 8530 8531 241 239 8289 8291 8988 8775 265 257 8747 8536 0 0 1618 1393 124 99 100 100 100 100 16580 17283 1 1 .976 1.017 1.013 1.304 52 230 .993 .97 80 2760 6850 41 49 132 140 0 7981 224 7756 .936 8209 7985 1.069 .913 -.096 -.131
7 450 133 217 214 232 -81 475 119 228 227 258 -95 0 0 151 57 88 71 82 1 69 1 151 163 null null null .372 .41 6.332 52 308 -1 -1 90 2910 6840 39 48 146 155 -50 124 200 -76 null 111 -89 null null null null
8 22610 20585 208 211 22401 20373 23020 21017 219 224 22811 20805 0 0 3720 3115 71 76 100 100 100 100 42774 43616 1.1 .909 .912 .912 .904 1.068 32 210 .913 .98 70 3060 6830 39 46 162 169 0 19257 197 19058 .851 19661 19462 1.175 .853 -.233 -.229
9 229 129 211 199 17 -70 223 123 218 211 11 -76 0 0 56 53 72 79 15 3 1 0 -53 -65 null null null 3.311 2.666 2.683 52 295 1.96 .2 90 3200 6830 38 47 175 184 -50 121 186 -65 null 115 -71 null null null null
10 259 215 213 209 45 6 262 212 226 218 48 3 0 0 82 74 83 66 26 25 3 3 51 51 7.5 .133 .063 .663 .674 3.228 52 313 .512 .28 90 3350 6830 38 47 190 199 -50 201 196 6 .125 198 3 8.017 .058 -3.003 -4.096
11 523 584 211 211 312 372 531 582 222 218 320 370 0 0 94 97 78 72 96 100 93 100 684 690 .839 1.192 1.156 1.229 1.22 1.543 32 207 1.09 .73 70 3510 6850 41 48 207 214 0 546 197 348 1.115 544 346 .897 1.082 .158 .113
12 416 1106 203 202 212 903 398 1123 217 213 194 920 0 0 109 215 90 74 90 100 59 100 1115 1114 .235 4.259 4.742 4.469 4.023 1.749 52 249 4.484 .75 80 3660 6850 41 49 222 230 0 1035 189 845 3.985 1051 861 .251 4.436 1.994 2.149
13 419 244 215 205 203 39 411 246 221 211 195 41 0 0 102 71 71 64 93 28 65 9 242 236 5.205 .192 .21 .289 .296 2.448 32 167 .247 .35 60 3820 6830 40 46 239 245 0 228 192 36 .18 230 38 5.564 .197 -2.476 -2.346
14 304 215 208 202 95 13 296 222 219 210 87 20 0 0 82 64 71 62 55 28 32 1 108 107 7.308 .137 .23 .826 .729 3.99 52 295 .271 .1 90 3960 6830 38 47 251 260 -50 201 189 12 .128 208 19 7.812 .215 -2.966 -2.217
15 245 62 207 206 37 -144 253 48 218 212 45 -158 0 0 64 50 74 66 26 1 3 0 -107 -113 null null null 5.654 7.721 2.884 52 291 .063 .05 90 4110 6830 38 47 266 275 -50 58 193 -135 null 45 -148 null null null null
16 1860 1021 212 215 1648 805 2316 1228 223 222 2104 1013 0 0 928 485 83 67 86 82 80 80 2453 3117 2.047 .488 .481 .534 .5 1.723 52 272 .491 .93 90 4260 6840 39 48 281 290 0 955 201 753 .457 1149 948 2.188 .45 -1.13 -1.151
17 270 117 208 209 61 -92 281 102 220 219 72 -107 0 0 74 62 91 74 25 1 5 1 -31 -35 null null null 1.64 1.622 2.411 52 291 -1 -1 90 4410 6830 38 47 296 305 -50 109 196 -86 null 95 -100 null null null null
18 231 82 204 222 26 -140 227 71 256 242 22 -151 0 0 64 60 347 133 0 0 0 0 -114 -129 null null null 4.887 5.806 2.825 52 311 .344 .5 90 4560 6830 38 47 311 320 -50 77 208 -131 null 66 -141 null null null null
19 434 245 217 213 216 32 423 247 274 246 205 34 0 0 92 53 406 152 6 0 0 0 248 239 6.75 .148 .166 .163 .217 3.665 32 220 .244 .62 70 4720 6830 39 46 328 335 0 229 199 30 .139 231 32 7.216 .155 -2.851 -2.688
20 1500 2823 218 203 1282 2619 1721 3209 224 213 1502 3006 0 0 654 1043 70 66 92 98 90 98 3901 4508 .489 2.043 2.001 2.501 2.065 2.276 52 267 1.976 .96 80 4860 6830 39 47 342 350 0 2641 190 2450 1.911 3002 2812 .523 1.872 .934 .905

Total number of rows: 44544

Table truncated, full table size 9676 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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