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Sample GSM989737 Query DataSets for GSM989737
Status Public on Aug 23, 2012
Title PC 252N
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 252N2
Organism Homo sapiens
Characteristics individual: PC 252N
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/2008-08/81100.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 18283 41605 163 117 18119 41487 22196 49507 175 128 22033 49389 0 0 7341 16738 64 60 100 100 100 100 59606 71422 .437 2.29 2.242 2.31 2.293 1.099 32 230 2.354 .97 70 1770 4930 21 28 37 44 0 39466 111 39354 2.172 46962 46850 .46 2.126 1.119 1.088
2 14855 34613 151 116 14703 34497 16671 41912 167 145 16520 41796 0 0 7596 18492 63 114 100 100 100 100 49200 58316 .426 2.346 2.53 2.087 2.287 1.664 32 220 2.43 .97 70 1910 4920 20 27 51 58 0 32834 110 32724 2.226 39757 39647 .449 2.4 1.154 1.263
3 8736 10049 157 94 8579 9954 7096 6658 173 131 6939 6564 0 0 7954 9052 80 116 86 86 76 82 18533 13503 .862 1.16 .946 1.243 1.201 2.71 52 291 1.155 .97 80 2060 4920 20 28 66 74 0 9532 89 9442 1.101 6316 6227 .909 .897 .138 -.156
4 18474 44223 180 131 18294 44092 21307 51556 200 157 21127 51425 0 12 6828 19255 111 109 100 100 100 100 62386 72552 .415 2.41 2.434 2.102 2.458 1.741 32 230 2.518 .97 70 2210 4920 20 27 81 88 0 41950 124 41825 2.286 48906 48781 .437 2.309 1.193 1.207
5 1066 417 154 96 911 320 1078 437 169 121 923 340 0 0 367 140 61 89 100 93 100 84 1231 1263 2.847 .351 .368 .335 .334 1.431 32 171 .323 .85 60 2360 4920 21 27 97 103 0 396 91 304 .333 415 323 3.001 .349 -1.586 -1.517
6 4637 6432 173 107 4464 6324 1915 2569 196 145 1741 2461 0 0 4650 6397 96 116 96 98 80 86 10788 4202 .706 1.417 1.414 1.573 1.477 1.508 80 392 1.404 .98 100 2520 4920 19 29 111 121 0 6101 101 5999 1.344 2437 2334 .744 1.341 .426 .423
7 456 232 147 107 308 124 462 212 169 121 315 104 0 0 136 62 67 70 100 83 83 33 432 419 2.484 .403 .33 .405 .416 2.056 12 68 .343 .56 40 2670 4920 22 26 129 133 0 220 101 118 .382 201 99 2.618 .313 -1.389 -1.675
8 21497 25259 172 89 21325 25169 23409 27008 181 106 23237 26918 0 0 6844 7409 85 95 100 100 100 100 46494 50155 .847 1.18 1.158 1.19 1.164 1.318 32 234 1.167 .97 70 2810 4920 20 27 141 148 0 23961 84 23875 1.12 25620 25534 .893 1.099 .163 .136
9 262 159 147 72 115 86 251 148 160 87 103 75 0 0 91 58 64 50 75 75 34 31 201 178 1.337 .748 .728 .672 .616 2.623 32 171 .57 .33 60 2960 4920 21 27 157 163 0 151 68 82 .709 140 71 1.41 .691 -.495 -.534
10 289 524 145 69 144 455 288 521 156 74 143 451 0 0 79 125 63 34 87 100 53 100 599 594 .316 3.16 3.154 3.667 2.908 2.634 32 214 3.553 .55 70 3120 4920 20 27 172 179 0 497 65 432 2.997 494 428 .334 2.992 1.584 1.581
11 571 676 161 65 410 611 582 684 174 75 421 619 0 0 128 238 78 53 100 100 96 96 1021 1040 .671 1.49 1.47 1.421 1.38 1.317 32 176 1.699 .86 60 3270 4920 21 27 188 194 0 641 62 580 1.414 649 587 .707 1.395 .499 .48
12 432 843 165 69 267 773 442 816 183 84 276 747 0 0 117 186 83 58 96 100 78 100 1040 1023 .345 2.895 2.707 3.171 2.718 1.59 32 176 3.22 .74 60 3420 4910 20 26 203 209 0 800 65 733 2.746 774 709 .364 2.567 1.457 1.36
13 388 334 139 74 248 259 394 333 149 80 254 258 0 0 121 93 57 42 96 100 84 100 507 512 .958 1.044 1.016 1.06 .945 1.667 32 233 .977 .71 70 3570 4920 20 27 217 224 0 317 70 246 .991 316 245 1.009 .964 -.014 -.054
14 369 391 146 71 223 320 368 368 156 73 222 297 0 0 104 154 49 33 100 100 91 100 543 519 .697 1.435 1.338 1.466 1.747 1.492 12 104 1.417 .71 50 3710 4910 20 25 232 237 0 371 67 304 1.361 349 282 .735 1.269 .445 .344
15 245 72 139 64 105 8 226 52 157 75 86 -12 0 0 97 115 142 58 28 5 5 3 113 74 13.125 .076 null .323 .363 4.159 52 346 1.17 .39 90 3860 4910 18 27 245 254 -50 68 61 8 .072 49 -11 13.836 null -3.79 null
16 2635 1697 134 62 2500 1634 2669 1646 143 72 2534 1584 0 0 457 373 50 38 100 100 100 100 4134 4118 1.53 .654 .625 .647 .617 1.094 32 234 .658 .95 70 4020 4910 19 26 262 269 0 1610 59 1550 .62 1561 1503 1.613 .593 -.69 -.754
17 258 149 146 59 112 89 256 155 207 77 110 95 0 0 80 51 490 65 0 65 0 21 201 205 1.258 .795 .864 1.066 .819 3.55 32 171 .753 .46 60 4170 4910 20 26 278 284 0 141 56 84 .754 147 90 1.327 .819 -.408 -.288
18 197 54 144 62 53 -8 193 47 178 74 49 -14 0 0 64 24 357 46 0 3 0 0 45 35 null null null .37 .307 3.254 52 325 .27 .36 90 4320 4910 18 27 291 300 -50 51 59 -8 null 45 -13 null null null null
19 479 308 146 66 333 242 485 279 157 73 338 213 0 0 181 116 49 36 93 100 93 96 575 551 1.376 .727 .63 .746 .754 1.796 32 176 .7 .74 60 4480 4910 20 26 309 315 0 292 63 230 .689 265 202 1.451 .598 -.537 -.742
20 2144 6707 144 72 2000 6635 2330 7667 153 79 2186 7595 0 0 788 2631 51 40 100 100 100 100 8635 9781 .301 3.318 3.474 3.221 3.324 1.282 32 226 3.468 .96 70 4620 4900 18 25 322 329 0 6362 68 6294 3.147 7273 7205 .318 3.296 1.654 1.721

Total number of rows: 44544

Table truncated, full table size 9494 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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