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Sample GSM252346 Query DataSets for GSM252346
Status Public on Dec 01, 2008
Title Human Prostate 686
Sample type RNA
 
Channel 1
Source name Reference
Organism Homo sapiens
Characteristics Reference
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.
Label Cy5
Label protocol Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCap, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
 
Channel 2
Source name Human Prostate 686 treated with Immediate Radical Prostatectomy
Organism Homo sapiens
Characteristics Human Prostate 686. #: 686; Treatment: Immediate Radical Prostatectomy; Reference: HGSv5;
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.
Label Cy3
Label protocol Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCap, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
 
 
Hybridization protocol Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Nelson PS, Pritchard C, Abbott D, and Clegg N. The human (PEDB) and mouse (mPEDB) Prostate Expression Databases. Nucleic Acids Res 2002;30:218-220 and Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
Scan protocol Fluorescence array images were collected using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA) and processed as we have previously described in True L, Coleman I, Hawley S, et al. A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A 2006;103:10991-10996.
Description Human Prostate 686 from Human hybridized against Reference
Data processing Changes in gene expression were evaluated using the Statistical Analysis of Microarray (SAM) program (http://www-stat.stanford.edu/_tibs/SAM/) to perform a one-sample t-test assessing the effect of Acyline treatment on gene expression (22). An FDR (false discovery rate) of less than 5% was considered significant. Quantile normalization was performed in Bioconductor (23) to allow single channel comparison of the absolute signal intensities in the experimental channel across different arrays in the same experiment.
 
Submission date Dec 19, 2007
Last update date Dec 28, 2007
Contact name Denise Mauldin
E-mail(s) [email protected]
Phone 2066673480
Fax 2066672917
URL http://www.pedb.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Peter Nelson
Street address 1100 Fairview Ave N D4-100
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL4768
Series (1)
GSE9983 Prostate Cancer Gene Expression Changes with Neoadjuvant Hormone Therapy

Data table header descriptions
ID_REF the unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
VALUE normalized log (experiment/reference) ratio data comparable across rows and samples
MetaCol Column referring to overall organization
MetaRow Row referring to overall organization
Column the column number of the feature.
Row the row number of the feature.
Name the name of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
X the X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. the diameter in µm of the feature-indicator.
F635 Median median feature pixel intensity at wavelength #1 (635 nm).
F635 Mean mean feature pixel intensity at wavelength #1 (635 nm).
F635 SD the standard deviation of the feature pixel intensity at wavelength #1 (635 nm).
F635 CV the coefficient of variation of feature pixel intensity.
B635 the actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B635 is different to B635 Median
B635 Median the median feature background intensity at wavelength #1 (635 nm).
B635 Mean the mean feature background intensity at wavelength #1 (635 nm).
B635 SD the standard deviation of the feature background intensity at wavelength #1 (635 nm).
B635 CV the coefficient of variation of background pixel intensity.
% > B635+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
% > B635+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of feature pixels at wavelength 635 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm).
F532 CV the coefficient of variation of feature pixel intensity.
B532 the actual background value used for the feature in GenePix Pro calculations (as opposed to B532 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B532 is different to B532 Median.
B532 Median the median feature background intensity at wavelength #2 (532 nm).
B532 Mean the mean feature background intensity at wavelength #2 (532 nm).
B532 SD the standard deviation of the feature background intensity at wavelength #2 (532 nm).
B532 CV the coefficient of variation of background pixel intensity.
% > B532+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
% > B532+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. the percentage of feature pixels at wavelength 532 that are saturated.
Ratio of Medians (635/532) the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (635/532) the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios (635/532) the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (635/532) the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio (635/532) the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R2 (635/532) the coefficient of determination for the current regression value.
F Pixels the total number of feature pixels.
B Pixels the total number of background pixels.
Circularity a measure of circularity from 0 to 100, using a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular. Circular features always have a circularity of 100, square features always have a circularity of 79 (
Sum of Medians (635/532) the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means (635/532) the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio (635/532) log (base 2) transform of the ratio of the medians.
F635 Median - B635 the median feature pixel intensity at 635 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at 532 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at 635 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at 532 with the median background subtracted.
F635 Total Intensity the sum of all pixel intensities in the feature at wavelenth 635.
F532 Total Intensity the sum of all pixel intensities in the feature at wavelenth 532.
SNR 635 the signal-to-noise ratio of the feature, calculated as (F635 Mean - B635 Mean)/B635 SD.
SNR 532 the signal-to-noise ratio of the feature, calculated as (F532 Mean - B532 Mean)/B532 SD.
Flags the type of flag associated with a feature.
Normalize the normalization status of the feature (included/not included).
Autoflag reports whether or not a feature has been flagged from the Flag Features dialog box. It applies to good and bad flags only.

Data table
ID_REF VALUE MetaCol MetaRow Column Row Name X Y Dia. F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) F Pixels B Pixels Circularity Sum of Medians (635/532) Sum of Means (635/532) Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize Autoflag
237241 -0.859740677 1 1 1 1 gi|220150|gb|D90427|D90427 3090 9600 120 3338 3453 711 20 788 788 810 216 26 99 99 0 1920 1973 715 36 256 256 272 114 41 100 98 0 1.532 1.552 1.568 1.651 1.819 1.523 0.731 120 658 100 4214 4382 0.616 2550 1664 2665 1717 414320 236749 12.236 14.921 0 0 0
237242 -1.632346373 1 1 2 1 gi|179280|gb|M27132.1|HUMATPSYB 3290 9590 100 8274 8657 4737 54 758 758 768 242 31 97 95 0 2887 3291 2062 62 251 251 266 129 48 91 88 0 2.851 2.598 2.487 3.164 2.285 2.565 0.807 80 473 100 10152 10939 1.512 7516 2636 7899 3040 692592 263282 32.599 23.450 0 0 0
237243 1 1 3 1 gi|12420723|gb|BG030944|BG030944 3480 9590 140 741 752 144 19 718 718 731 197 26 13 1 0 257 265 64 24 243 243 257 99 38 8 1 0 1.643 1.545 2.472 2.478 4.299 16.331 0.018 156 839 100 37 56 0.716 23 14 34 22 117274 41288 0.107 0.081 -50 0 0
237244 -0.987868084 1 1 4 1 gi|21536438|ref|NM_012161.2| 3670 9600 100 2546 2650 553 20 767 767 786 289 36 100 100 0 1073 1121 386 34 247 247 257 60 23 100 98 0 2.154 2.154 2.113 2.345 2.012 2.580 0.506 80 491 100 2605 2757 1.107 1779 826 1883 874 212036 89701 6.450 14.400 0 0 0
237245 -1.084815764 1 1 5 1 gi|21536438|ref|NM_012161.2| 3880 9610 100 2765 2748 536 19 735 735 743 169 22 100 100 0 1277 1351 388 28 244 244 254 56 22 100 100 0 1.965 1.818 2.010 1.855 1.585 1.910 0.698 80 456 100 3063 3120 0.975 2030 1033 2013 1107 219840 108109 11.864 19.589 0 0 0
237246 1 1 6 1 gi|14065685|gb|BG755019|BG755019 4060 9590 140 727 765 512 66 707 707 749 746 99 1 0 0 251 265 88 33 240 240 254 212 83 3 1 0 1.818 2.320 3.146 2.798 4.981 9.841 0.111 156 805 100 31 83 0.862 20 11 58 25 119271 41333 0.021 0.052 -50 0 0
237247 1 1 7 1 gi|15996756|gb|BI856009|BI856009 4260 9590 140 704 711 146 20 696 696 735 765 104 0 0 0 239 243 45 18 235 235 252 231 91 0 0 0 2.000 1.875 3.073 2.972 5.019 0.921 0.534 156 762 100 12 23 1.000 8 4 15 8 110937 37888 -0.031 -0.039 -50 0 0
237248 1 1 8 1 gi|19586973|gb|BM969386|BM969386 4450 9600 140 699 720 229 31 700 700 714 180 25 14 3 0 246 261 110 42 235 235 244 58 23 18 5 0 -0.091 0.769 4.639 3.497 4.081 6.012 0.090 156 824 100 10 46 Error -1 11 20 26 112361 40651 0.033 0.293 -50 0 0
237249 -1.499574585 1 1 9 1 gi|7703647|gb|AW771590| 4660 9610 100 11551 11957 5303 44 741 741 745 155 20 100 100 0 3844 3858 2007 52 243 243 252 63 25 97 96 0 3.002 3.103 3.131 3.663 2.432 3.246 0.688 80 465 100 14411 14831 1.586 10810 3601 11216 3615 956594 308664 72.335 57.238 0 0 0
237250 1 1 10 1 gi|20408448|gb|BQ227048|BQ227048 4850 9600 140 762 788 246 31 769 769 773 168 21 17 4 0 256 308 322 104 247 247 258 67 25 18 6 0 -0.778 0.311 3.086 2.941 6.179 1.296 0.090 156 835 100 2 80 Error -7 9 19 61 122967 48042 0.089 0.746 -50 0 0
237251 -0.408272909 1 1 11 1 gi|11012215|gb|AU150694|AU150694 5030 9600 110 4839 5328 2365 44 772 772 779 173 22 100 100 0 3699 3707 1394 37 244 244 267 212 79 97 96 0 1.177 1.316 1.169 1.389 2.218 1.175 0.609 80 535 100 7522 8019 0.235 4067 3455 4556 3463 426258 296544 26.295 16.226 0 0 0
237252 1 1 12 1 gi|17298590|gb|AC009167.8| 5240 9600 140 803 799 164 20 758 758 792 620 78 0 0 0 255 264 64 24 240 240 255 171 67 1 1 0 3.000 1.708 4.333 3.358 4.740 17.061 0.007 156 841 100 60 65 1.585 45 15 41 24 124660 41219 0.011 0.053 -50 0 0
237253 -1.402479466 1 1 13 1 gi|13477360|gb|BC005157|BC005157 5430 9620 120 2903 2883 906 31 765 765 774 159 20 95 93 0 1061 1079 384 35 240 240 246 49 19 99 98 0 2.604 2.524 2.580 2.473 2.435 2.861 0.696 120 571 100 2959 2957 1.381 2138 821 2118 839 345918 129537 13.264 17.000 0 0 0
237254 1 1 14 1 UNKNOWN_4 5630 9600 140 813 826 189 22 762 762 771 150 19 30 10 0 253 275 118 42 237 237 250 117 46 7 3 0 3.188 1.684 3.429 2.972 3.719 15.190 0.012 156 781 100 67 102 1.672 51 16 64 38 128818 42965 0.367 0.214 -50 0 0
237255 1 1 15 1 gi|5031976|ref|NM_005746.1| 5820 9600 140 774 828 246 29 740 740 746 180 24 26 9 0 261 275 92 33 234 234 245 109 44 13 4 0 1.259 2.146 3.105 2.782 3.862 7.103 0.139 156 751 100 61 129 0.333 34 27 88 41 129131 42934 0.456 0.275 -50 0 0
237256 1 1 16 1 gi|4827043|ref|NM_005121.1| 6020 9610 140 729 757 172 22 705 705 719 160 22 25 7 0 239 259 89 34 232 232 241 55 22 20 7 0 3.429 1.926 4.231 3.607 5.476 7.629 0.033 156 726 100 31 79 1.778 24 7 52 27 118072 40476 0.238 0.327 -50 0 0
237257 1 1 17 1 BLANK 6210 9610 140 724 746 171 22 710 710 723 182 25 15 4 0 246 287 175 60 236 236 247 76 30 16 10 0 1.400 0.706 2.062 1.959 4.929 5.571 0.026 156 898 100 24 87 0.485 14 10 36 51 116379 44796 0.126 0.526 -50 0 0
237258 0.005633962 1 1 18 1 UNKNOWN_6 6470 9630 50 2755 3048 2044 67 736 736 757 175 23 91 83 0 2594 6387 7433 116 249 249 275 127 46 83 66 0 0.861 0.377 0.695 0.826 12.963 0.098 0.070 12 84 100 4364 8450 -0.216 2019 2345 2312 6138 36571 76648 13.091 48.126 0 0 0
237259 0.247910991 1 1 19 1 gi|14042897|gb|AK027893|AK027893 6590 9620 130 5522 5655 2051 36 706 706 716 169 23 98 98 0 5727 6555 3314 50 240 240 253 86 33 100 100 0 0.878 0.784 0.853 0.747 2.169 0.705 0.648 120 731 100 10303 11264 -0.188 4816 5487 4949 6315 678548 786619 29.225 73.279 0 0 0
237260 1 1 20 1 gi|5901981|ref|NM_006899.1| 6800 9610 140 743 823 506 61 720 720 748 423 56 5 3 0 244 280 167 59 239 239 250 64 25 18 8 0 4.600 2.512 4.004 3.595 3.377 17.994 0.087 156 810 100 28 144 2.202 23 5 103 41 128436 43752 0.177 0.469 -50 0 0

Total number of rows: 15488

Table truncated, full table size 4205 Kbytes.




Supplementary file Size Download File type/resource
GSM252346.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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