NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989767 Query DataSets for GSM989767
Status Public on Aug 23, 2012
Title PC 629N
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 629N2
Organism Homo sapiens
Characteristics individual: PC 629N
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/2008-08/81071.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 9159 18671 67 66 9091 18604 10316 18712 72 79 10248 18645 0 0 3635 14647 23 55 100 100 100 100 27695 28893 .489 2.046 1.819 1.211 2.39 3.646 32 236 2.705 .89 70 1730 7030 27 34 45 52 0 16725 59 16665 1.833 16762 16702 .546 1.63 .874 .705
2 7868 15137 67 72 7800 15065 8269 13431 75 87 8202 13359 0 0 4072 13218 27 75 100 100 100 96 22865 21561 .518 1.931 1.629 .924 1.832 4.325 32 228 2.493 .9 70 1880 7030 27 34 60 67 0 13560 64 13495 1.73 12031 11967 .578 1.459 .791 .545
3 2999 3098 67 72 2931 3026 3269 1333 70 76 3201 1261 0 0 1699 3055 21 36 100 90 100 81 5957 4462 .969 1.032 .394 .475 .95 5.031 32 176 1.339 .89 60 2020 7020 27 33 75 81 0 2775 64 2711 .925 1194 1130 1.081 .353 -.113 -1.503
4 8671 18822 71 76 8600 18746 9715 21089 76 89 9644 21013 0 0 4195 14303 25 59 100 96 100 93 27346 30657 .459 2.18 2.179 1.286 2.197 4.083 32 227 2.72 .88 70 2170 7020 26 33 89 96 0 16861 68 16793 1.953 18891 18823 .512 1.952 .965 .965
5 318 161 69 70 249 90 318 165 72 76 248 94 0 0 57 59 21 39 100 83 100 58 339 342 2.767 .361 .379 .341 .369 2.585 12 104 .278 .48 50 2320 7030 28 33 105 110 0 144 63 81 .324 148 84 3.088 .34 -1.627 -1.558
6 1947 3128 69 72 1877 3056 2138 3517 74 82 2069 3445 0 0 822 2390 24 46 100 94 100 88 4933 5514 .614 1.628 1.665 .828 1.771 5.096 52 286 2.066 .9 80 2480 7020 26 34 120 128 0 2802 64 2738 1.458 3151 3086 .686 1.492 .544 .577
7 120 93 71 69 49 23 106 92 75 80 35 22 0 0 46 49 24 47 69 23 44 9 72 57 2.13 .469 .629 .922 .89 3.291 52 342 2.565 .17 90 2630 7020 25 34 134 143 -50 83 62 21 .42 82 20 2.378 .563 -1.25 -.829
8 3907 4480 69 74 3837 4406 4271 4437 74 81 4201 4363 0 0 1362 3043 23 46 100 96 100 96 8243 8564 .871 1.148 1.039 .686 1.379 4.428 32 217 1.376 .85 70 2780 7020 26 33 150 157 0 4013 66 3947 1.029 3975 3908 .972 .93 .041 -.104
9 119 158 67 66 52 91 114 162 72 74 46 95 0 0 35 48 23 39 75 83 50 75 143 141 .571 1.75 2.065 1.839 2.368 4.122 12 104 3.66 .28 50 2930 7030 28 33 166 171 0 142 59 82 1.568 145 85 .638 1.85 .649 .888
10 105 184 63 52 41 132 109 176 66 59 46 123 0 0 33 100 18 33 65 81 59 68 173 169 .311 3.22 2.674 3.749 4.145 4.306 32 162 5.622 .43 60 3090 7030 28 34 182 188 0 165 47 118 2.884 158 110 .347 2.395 1.528 1.26
11 198 344 61 55 136 288 190 345 65 63 129 289 0 0 63 170 19 35 100 96 93 87 424 418 .472 2.118 2.24 1.898 2.251 3.017 32 210 2.778 .68 70 3230 7020 26 33 195 202 0 308 49 258 1.897 309 259 .527 2.007 .924 1.005
12 207 314 61 61 145 252 204 337 66 72 143 276 0 0 80 168 20 44 93 87 87 75 397 419 .575 1.738 1.93 1.672 1.678 2.845 32 175 2.098 .74 60 3380 7010 26 32 211 217 0 281 55 226 1.557 302 247 .642 1.729 .639 .79
13 139 167 68 54 70 112 128 167 75 70 59 112 0 0 43 78 29 59 83 66 50 41 182 171 .625 1.6 1.898 1.338 1.313 3.081 12 104 2.744 .48 50 3530 7010 26 31 226 231 0 150 48 100 1.433 150 100 .698 1.7 .519 .766
14 146 205 68 68 78 136 131 158 75 80 62 89 0 0 56 141 37 61 83 75 33 33 214 151 .574 1.744 1.435 1.999 2.392 4.18 12 104 5.558 .33 50 3680 7010 26 31 241 246 0 184 61 122 1.562 142 80 .64 1.286 .643 .363
15 71 63 65 68 6 -5 69 53 69 80 4 -15 0 0 18 50 22 58 13 3 5 3 1 -11 null null null 1.609 2.544 4.55 52 334 10.83 .15 90 3830 7010 24 33 254 263 -50 56 61 -4 null 47 -13 null null null null
16 269 290 74 59 195 231 278 268 74 76 204 209 0 0 66 151 24 63 100 84 100 75 426 413 .844 1.185 1.025 1.127 1.335 2.426 32 169 1.443 .75 60 3990 7020 27 33 272 278 0 260 53 207 1.061 240 187 .942 .918 .086 -.124
17 99 190 67 69 31 120 95 150 72 81 27 80 0 0 34 184 25 44 50 58 33 41 151 107 .258 3.871 2.963 1.798 2.127 10.228 12 104 4.677 .68 50 4120 7020 27 32 285 290 0 170 62 107 3.468 134 72 .288 2.654 1.794 1.408
18 72 66 68 68 3 -2 69 60 74 80 0 -8 0 0 21 40 25 51 17 7 1 3 1 -8 null null null 2.041 2.248 5.899 52 320 12.951 .11 90 4280 7020 25 34 299 308 -50 59 61 -2 null 54 -7 null null null null
19 147 172 66 68 80 103 149 167 71 83 82 98 0 0 41 84 23 50 90 65 78 46 183 180 .777 1.288 1.195 1.128 1.559 4.636 32 174 3.313 .23 60 4440 7020 27 33 317 323 0 154 61 92 1.153 150 88 .867 1.071 .206 .098
20 935 3466 67 63 867 3403 1064 3679 70 72 996 3616 0 0 355 2238 21 38 100 96 100 96 4270 4612 .255 3.925 3.631 2.698 4.413 3.851 32 225 5.101 .85 70 4590 7010 25 32 331 338 0 3105 56 3048 3.516 3296 3239 .284 3.252 1.814 1.701

Total number of rows: 44544

Table truncated, full table size 9294 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap