NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM147343 Query DataSets for GSM147343
Status Public on Jan 11, 2009
Title Normal prostate vs. 24670N (normal adjacent to tumor)
Sample type other
 
Channel 1
Source name Normal prostate reference control
Organism Homo sapiens
Characteristics Normal prostate tissue from 70 year old male. Sample was enriched for microRNA fraction.
Biomaterial provider Ambion Inc. (Austin, TX)
Treatment protocol NA
Growth protocol NA
Extracted molecule other
Extraction protocol MicroRNA was isolated from the tissue sample using the mirVana microRNA isolation kit from Ambion.
Label Cy3
Label protocol Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere Inc.
 
Channel 2
Source name Prostate normal adjacent to tumor, sample 24670N
Organism Homo sapiens
Characteristics Normal adjacent to tumor prostatic tissue from radical prostatectomy specimen. Sample was enriched for the microRNA fraction.
Biomaterial provider UCSF Tissue Core Facility
Treatment protocol NA
Growth protocol NA
Extracted molecule other
Extraction protocol MicroRNA was isolated from the tissue sample using the mirVana microRNA isolation kit from Ambion.
Label Cy5
Label protocol Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere Inc.
 
 
Hybridization protocol Briefly, 200 ng of enriched miRNA was labeled and hybridized in the supplied 2X SDS based hybridization buffer to the arrays at 46 degrees Celsius for 16 hours in a Hybex hybridization oven (SciGene). Arrays were washed as follows: Cover slips were floated off in wash 1 (2X SSC, 0.2% SDS pre-warmed to 42 degrees Celsius), arrays were then washed in pre-warmed wash #1 for 15 minutes, rinsed in wash #2 (2X SSC) for 10 minutes at room temperature, and rinsed in wash #3 (0.2X SSC) for 10 minutes at room temperature. Slides were then dried in a centrifuge. The 3DNA Capture Reagent was then hybridized to the arrays for 4 hours at 60 degrees Celsius. Washes were performed as above with the exception that wash #1 was pre-warmed to 60 degrees Celsius
Scan protocol Images were acquired using an Axon 4000b confocal laser scanner with Genepix 3.0 software (Axon, Foster City, CA).
Description Quantitations are based on the images (ratios of median fluorescence intensity were the primary study measurements). Genepix 3.0 produces both feature and background intensity and ratio measurements for the Cy3 and Cy5 channels and notes if data are flagged by the analyst.
Data processing Only Genepix median ratios for non-flagged spots were used for the analysis. Genepix data was uploaded to the NOMAD relational database (http://derisilab.ucsf.edu), median ratio information was downloaded after linear normalization of Cy3 and Cy5 signals (equal average intensity of each fluorescent channel). Data were formatted for the Cluster (http://rana.lbl.gov) algorithm, which was used after log base 2 transformation of ratios, and filtering to exclude genes flagged in more than 20% of the arrays.
 
Submission date Nov 28, 2006
Last update date Oct 07, 2008
Contact name Michael D. Mattie
E-mail(s) mdmattie@yahoo.com
Phone 919-483-5617
Fax 919-315-0158
Organization name GlaxoSmithKline
Department Genomics Research
Lab Quantitative Expression
Street address Five Moore Drive
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL3238
Series (1)
GSE6636 Prostate miRNA expression profiles

Data table header descriptions
ID_REF
Ratio the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
F635 Median the median feature pixel intensity at wavelength #1 (635 nm)
F635 Mean the mean feature pixel intensity at wavelength #1 (635 nm)
F635 SD the standard deviation of the feature pixel intensity at wavelength #1 (635 nm)
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+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 #1 that are saturated
F532 Median the median feature pixel intensity at wavelength #2 (532 nm)
F532 Mean the mean feature pixel intensity at wavelength #2 (532 nm)
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm)
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+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 #2 that are saturated
Ratio of means the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted
Mean of Ratios the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R? 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.
Sum of Medians the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
VALUE the same as UNF_VALUE but with flagged values removed
F635 Median - B635 the median feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at wavelength #2 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at wavelength #2 with the median background subtracted.
Flags the type of flag associated with a feature. -100: spots flagged as bad; -50: saturated spots; 0: unflagged, acceptable spots; 100: good spots.
UNF_Value log (base 2) transform of the ratio of the medians.

Data table
ID_REF Ratio F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R? F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags UNF_Value
BUFFER1 1 76 86 47 78 97 83 5 1 0 47 51 21 49 69 58 3 0 0 4 2.706 2.367 4.546 3.146 0.062 156 871 -4 10 0 -2 -2 8 2 -50 0
BUFFER2 -0.073 92 111 73 95 128 127 5 1 0 124 165 135 83 124 110 34 9 0 0.195 0.738 0.794 3.724 0.803 0 52 264 38 98 -3 41 16 82 -50
BUFFER3 0.5 80 91 57 81 102 96 7 1 0 46 59 45 48 73 75 7 2 0 0.909 2.727 2.356 5.247 3.299 0.005 156 607 -3 21 -1 -1 -2 10 11 -50 -1
BUFFER4 0.571 85 117 124 81 94 72 15 11 0 55 66 34 48 59 39 13 7 0 2 2.531 2.841 4.679 19.737 0.025 156 541 11 54 -0.807 4 7 36 18 -50 -0.807
BUFFER5 0 76 86 51 76 85 45 12 4 0 45 51 31 45 53 29 8 6 0 1.667 2.5 2.699 4.249 7.28 0.003 156 539 0 16 0 0 10 6 -50
BUFFER6 100000 70 76 34 75 102 157 0 0 0 44 51 24 44 87 341 0 0 0 0.143 4.333 3.313 4.15 26.602 0.001 156 538 -5 8 16.61 -5 0 1 7 -50 16.61
BUFFER7 4 81 104 83 77 120 199 4 1 0 46 91 246 45 106 372 2 0 0 0.587 2.687 2.495 4.248 0.406 0.842 156 549 5 73 2 4 1 27 46 -50 2
BUFFER8 4 86 155 242 78 112 158 10 5 0 48 126 403 46 92 243 5 3 0 0.962 2.556 2.037 5.638 0.611 0.329 156 547 10 157 2 8 2 77 80 -50 2
BUFFER9 3.5 81 92 57 74 88 69 9 4 0 46 54 31 44 55 39 8 3 0 1.8 3 3.275 3.635 18.236 0.004 156 561 9 28 1.807 7 2 18 10 -50 1.807
BUFFER10 -0.5 76 91 77 77 94 83 6 3 0 46 57 33 44 57 45 10 5 0 1.077 3.333 2.242 5.927 0.056 0.002 80 339 1 27 -1 2 14 13 -50
BUFFER11 7 76 88 51 83 110 98 6 1 0 46 54 36 47 72 68 5 1 0 0.714 2.912 2.67 3.759 4.693 0.027 156 589 -8 12 2.807 -7 -1 5 7 -50 2.807
BUFFER12 -9 87 119 93 96 141 136 8 3 0 53 88 71 52 91 84 18 6 0 0.639 2 1.685 5.032 2.598 0.079 156 534 -8 59 -9 1 23 36 -50
BUFFER13 100000 92 129 132 94 157 261 5 0 0 50 69 54 50 84 199 1 0 0 1.842 3.25 2.972 3.893 0.559 0.28 156 608 -2 54 16.61 -2 0 35 19 -50 16.61
BUFFER14 1.25 83 107 82 88 146 281 2 0 0 45 50 23 49 80 224 0 0 0 19 3.774 3.734 3.832 0.403 0.565 120 466 -9 20 0.322 -5 -4 19 1 -50 0.322
BUFFER15 100000 77 101 113 81 109 122 7 1 0 46 49 15 46 56 34 5 1 0 6.667 3.407 3.047 3.917 209.644 0 156 630 -4 23 16.61 -4 0 20 3 -50 16.61
BUFFER16 6 84 105 93 78 99 90 9 3 0 47 51 21 46 57 52 5 0 0 5.4 3.556 3.295 3.933 72.441 0.003 156 587 7 32 2.585 6 1 27 5 -50 2.585
BUFFER17 100000 80 100 105 77 110 146 4 1 0 46 52 22 46 57 51 4 0 0 3.833 3 2.529 4.031 14.891 0.048 156 557 3 29 16.61 3 0 23 6 -50 16.61
BUFFER18 100000 87 111 153 76 103 123 5 1 0 46 51 38 46 55 43 2 1 0 7 4.5 3.63 3.969 17.17 0.031 156 612 11 40 16.61 11 0 35 5 -50 16.61
BUFFER19 100000 78 105 108 76 94 90 12 4 0 46 56 41 46 53 40 10 4 0 2.9 2.747 2.973 5.732 7.102 0.098 156 641 2 39 16.61 2 0 29 10 -50 16.61
BUFFER20 11 87 115 108 76 95 79 14 8 0 47 57 33 46 54 49 8 3 0 3.545 4.25 3.832 4.317 68.288 0.001 156 683 12 50 3.459 11 1 39 11 -50 3.459

Total number of rows: 768

Table truncated, full table size 105 Kbytes.




Supplementary file Size Download File type/resource
GSM147343.gpr.gz 42.2 Kb (ftp)(http) GPR

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap