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Sample GSM153784 Query DataSets for GSM153784
Status Public on Jan 11, 2009
Title Normal prostate vs. 44652CC (young-car crash trauma)
Sample type other
 
Channel 1
Source name Normal prostate
Organism Homo sapiens
Characteristics Normal prostate reference control. RNA was isolated from prostate tissue of a 70 year old male without prostate cancer and enriched for the microRNA fraction.
Biomaterial provider Ambion
Treatment protocol NA
Growth protocol NA
Extracted molecule other
Extraction protocol MicroRNA was isolated from the tissue sample using the mirVana miRNA isolation kit from Ambion
Label Cy3
Label protocol Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere.
 
Channel 2
Source name 44652CC (young-car crash trauma)
Organism Homo sapiens
Characteristics Normal prostate tissue from a young individual that died as a result of trauma (car crash). Prostate tissue was obtained through organ donation. RNA was isolated and enriched for the microRNA fraction.
Biomaterial provider UCSF Tissue Core
Treatment protocol NA
Growth protocol NA
Extracted molecule other
Extraction protocol MicroRNA was isolated from the tissue sample using the mirVana miRNA isolation kit from Ambion
Label Cy5
Label protocol Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere.
 
 
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 Jan 03, 2007
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 median intensity in foreground (Cy5 channel)
F635 Mean mean intensity in foreground (Cy5 channel)
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 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)
B532 Median the median feature background intensity at wavelength #2 (532 nm)
B532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
B532 SD the standard deviation of the feature 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.t
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 ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
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 0 110 131 89 110 127 76 16 5 0 45 58 33 46 64 44 14 4 0 1.75 4.182 2.957 5.029 13.175 0.004 156 808 -1 33 0 -1 21 12 -50
BUFFER2 2.8 124 154 114 110 141 132 14 4 0 54 78 57 49 69 46 25 12 0 1.517 2.946 2.725 4.966 0.005 0 156 622 19 73 1.485 14 5 44 29 -50 1.485
BUFFER3 1.333 113 135 79 109 153 148 5 1 0 51 74 49 48 66 45 28 9 0 1 3.273 3.758 4.145 11.42 0.041 52 213 7 52 0.415 4 3 26 26 -100 0.415
BUFFER4 -8 112 169 509 104 129 121 7 2 0 45 61 43 46 60 40 16 7 0 4.333 3.519 4.108 4.435 23.259 0.1 156 613 7 80 8 -1 65 15 -50
BUFFER5 5 112 125 64 107 122 101 8 2 0 46 59 34 45 62 48 17 3 0 1.286 2.348 1.843 5.567 23.883 0.005 156 544 6 32 2.322 5 1 18 14 -50 2.322
BUFFER6 -1 103 116 64 106 117 71 10 5 0 47 61 44 44 61 55 10 5 0 0.588 3 2.772 4.96 14.805 0.003 156 637 0 27 -3 3 10 17 -50
BUFFER7 100000 113 144 177 107 121 71 17 8 0 46 61 43 46 63 52 12 3 0 2.467 3.167 3.141 4.638 19.389 0.012 156 601 6 52 16.61 6 0 37 15 -50 16.61
BUFFER8 2 114 131 75 110 137 140 6 1 0 51 74 61 49 68 51 19 8 0 0.84 2.286 2.11 4.438 0.014 0.001 156 547 6 46 1 4 2 21 25 -50 1
BUFFER9 2 107 118 76 109 136 148 3 1 0 45 63 63 46 63 45 14 8 0 0.529 4.813 3.906 4.027 0.018 0.001 156 632 -3 26 1 -2 -1 9 17 -50 1
BUFFER10 -0.333 104 116 58 105 118 64 13 5 0 47 65 47 44 59 37 21 9 0 0.524 1.5 1.953 6.068 10.237 0.013 52 228 2 32 -1 3 11 21 -100
BUFFER11 -0.5 102 120 70 103 133 294 1 0 0 46 60 35 44 60 42 15 4 0 1.063 3.7 3.42 4.476 28.372 0.069 156 650 1 33 -1 2 17 16 -50
BUFFER12 -1.4 99 146 136 106 133 101 15 7 0 50 69 46 45 65 60 20 3 0 1.667 2.929 2.867 4.854 49.011 0 80 311 -2 64 -7 5 40 24 0
BUFFER13 8 120 142 81 112 139 109 17 3 0 50 68 49 49 72 55 14 5 0 1.579 3.662 3.507 4.401 0.019 0.001 156 600 9 49 3 8 1 30 19 -50 3
BUFFER14 1 114 196 699 111 137 101 15 5 0 52 73 69 49 67 45 22 6 0 3.542 3.167 3.235 4.606 49.068 0.023 156 556 6 109 0 3 3 85 24 -50 0
BUFFER15 -6 109 170 385 121 162 283 3 1 0 50 73 94 48 68 53 15 5 0 1.96 3 2.693 5.096 10.394 0.24 156 520 -10 74 -12 2 49 25 -50
BUFFER16 100000 114 140 103 120 165 286 2 0 0 48 70 56 48 71 67 14 5 0 0.909 3.72 2.85 4.082 74.186 0.001 156 555 -6 42 16.61 -6 0 20 22 -50 16.61
BUFFER17 -0.4 112 170 209 114 154 165 13 3 0 53 76 60 48 65 57 16 8 0 2 3.967 3.17 4.921 12.013 0.03 156 557 3 84 -2 5 56 28 -50
BUFFER18 -4 113 121 61 109 138 120 4 0 0 48 69 57 49 66 56 13 7 0 0.6 2.798 2.391 5.024 60.977 0.001 156 651 3 32 4 -1 12 20 -50
BUFFER19 -15 121 146 119 106 272 2250 0 0 0 47 78 78 48 78 256 1 0 0 1.333 7 3.499 8.608 9.14 0.914 52 258 14 70 15 -1 40 30 -100
BUFFER20 100000 101 113 66 108 193 1471 0 0 0 46 64 48 46 65 166 2 0 0 0.278 3.85 3.463 4.534 9.138 0.945 156 605 -7 23 16.61 -7 0 5 18 -50 16.61

Total number of rows: 768

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM153784.gpr.gz 44.2 Kb (ftp)(http) GPR

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