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Sample GSM102244 Query DataSets for GSM102244
Status Public on Apr 05, 2006
Title Normal prostate vs. LNCaP
Sample type other
 
Channel 1
Source name Normal prostate
Organism Homo sapiens
Characteristics Commerically obtained RNA from prostate tissue from a 79 year old male
Biomaterial provider Ambion
Extracted molecule other
Extraction protocol MicroRNA was isolated from the prostate tissue by Ambion (mirVana Isolation kit)
Label Cy3
Label protocol Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere Inc. A total of 750 ng of amplified material was labeled.
 
Channel 2
Source name LNCaP cells
Organism Homo sapiens
Characteristics Untreated LNCaP cells, hormone sensitive prostate cancer cell line
Biomaterial provider ATCC
Treatment protocol Untreated PC3 cells
Growth protocol Standard growth conditions
Extracted molecule other
Extraction protocol MicroRNA was isolated from the untreated LNCaP cells 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. A total of 750 ng of amplified material was labeled.
 
 
Hybridization protocol Briefly, 10 ng of enriched miRNA was amplified using a modification of the SenseAmp Plus protocol from Genisphere. A total of 750 ng of amplified material 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 Mar 29, 2006
Last update date Apr 05, 2006
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)
GSE4574 Normal vs. Tumor Prostate miRNA

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.
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 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.
UNF_VALUE1 log (base 2) transform of the ratio of the medians
UNF_VALUE the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.

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_VALUE1 UNF_VALUE
BUFFER1 -10 148 175 111 138 187 174 10 3 0 45 63 44 46 62 41 19 9 0 2.176 4.826 3.89 3.466 0.009 0.001 156 881 9 54 10 -1 37 17 -50
BUFFER2 100000 148 190 141 153 215 236 13 0 0 46 50 21 46 60 35 9 3 0 9.25 7.556 7.113 5.619 0.007 0.002 52 264 -5 41 -5 0 37 4 -50 16.60964047 16.61
BUFFER3 -2 155 190 192 151 191 153 11 3 0 44 54 36 46 63 47 8 3 0 4.875 6.25 4.933 4.369 45.786 0.005 156 607 2 47 4 -2 39 8 -50
BUFFER4 -4 141 169 111 145 184 141 12 3 0 46 65 47 45 61 44 19 8 0 1.2 5.826 3.746 5.777 674.029 0 156 541 -3 44 -4 1 24 20 -50
BUFFER5 100000 147 174 113 140 189 158 13 2 0 45 59 36 45 60 42 15 7 0 2.429 4.719 4.654 5.196 72.214 0.003 156 539 7 48 7 0 34 14 -50 16.60964047 16.61
BUFFER6 100000 139 179 141 151 192 146 11 3 0 46 61 39 46 61 45 17 4 0 1.867 5.54 4.513 4.847 0.012 0.001 156 538 -12 43 -12 0 28 15 -50 16.60964047 16.61
BUFFER7 1.667 164 201 130 159 208 183 12 1 0 48 78 67 45 61 45 26 11 0 1.273 5.273 4.521 6.664 0.004 0 156 549 8 75 0.737 5 3 42 33 -50 0.737254104 0.737
BUFFER8 100000 151 180 149 152 215 225 7 1 0 44 61 58 44 59 41 12 8 0 1.647 7.479 5.121 5.749 0.001 0 156 547 -1 45 -1 0 28 17 -50 16.60964047 16.61
BUFFER9 5 156 208 187 151 205 201 14 6 0 45 59 43 44 59 37 13 8 0 3.8 8.636 5.631 5.482 812.777 0 156 561 6 72 2.322 5 1 57 15 -50 2.321928095 2.322
BUFFER10 4.25 148 180 122 131 176 152 13 5 0 48 75 69 44 60 46 18 12 0 1.581 3.052 2.718 4.967 25.953 0.016 80 339 21 80 2.087 17 4 49 31 -50 2.087462841 2.087
BUFFER11 4.667 154 196 165 140 183 154 12 5 0 48 62 39 45 61 47 11 5 0 3.294 6.667 5.7 4.314 1469.816 0 156 589 17 73 2.222 14 3 56 17 -50 2.222495467 2.222
BUFFER12 -2 148 184 141 150 205 175 8 3 0 47 59 39 46 62 47 10 7 0 2.615 6.235 4.689 5.228 40.141 0.007 156 534 -1 47 -2 1 34 13 -50
BUFFER13 100000 155 183 134 146 197 183 9 3 0 46 64 51 46 64 53 14 5 0 2.056 6.414 5.427 4.366 26.202 0.015 156 608 9 55 9 0 37 18 -50 16.60964047 16.61
BUFFER14 -4.5 158 198 185 149 192 173 14 4 0 46 57 30 48 68 49 10 4 0 5.444 6.313 4.961 5.573 50.923 0.005 120 466 7 58 9 -2 49 9 -50
BUFFER15 14 167 207 164 139 181 140 17 7 0 48 60 33 46 66 50 12 4 0 4.857 4.5 4.112 5.596 0.007 0 156 630 30 82 3.807 28 2 68 14 -50 3.807354922 3.807
BUFFER16 -4 139 167 130 143 182 142 10 5 0 46 65 58 45 60 42 16 8 0 1.2 3.75 3.544 5.892 0.001 0 156 587 -3 44 -4 1 24 20 -50
BUFFER17 3.667 160 208 273 149 194 155 12 6 0 49 66 43 46 61 49 14 8 0 2.95 6.775 5.923 4.263 512.564 0 156 557 14 79 1.874 11 3 59 20 -50 1.874600266 1.874
BUFFER18 -4.5 144 187 138 162 205 156 13 3 0 51 73 51 47 67 57 19 8 0 0.962 4.638 4.302 4.31 44.699 0.004 156 612 -14 51 -18 4 25 26 -50
BUFFER19 26 187 238 173 161 209 176 19 8 0 48 67 50 47 66 49 16 9 0 3.85 7.25 4.456 6.024 0.003 0 156 641 27 97 4.7 26 1 77 20 -50 4.700439718 4.7
BUFFER20 1 161 221 225 158 217 197 13 3 0 51 70 48 48 69 50 16 7 0 2.864 5.881 5.423 5.09 0.014 0.003 156 683 6 85 0 3 3 63 22 -50 0 0

Total number of rows: 768

Table truncated, full table size 118 Kbytes.




Supplementary data files not provided
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