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Sample GSM102246 Query DataSets for GSM102246
Status Public on Apr 05, 2006
Title Normal prostate vs. needle core tumor
Sample type other
 
Channel 1
Source name Normal prostate
Organism Homo sapiens
Characteristics Commercially obtained RNA from prostate of 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 Needle core tumor
Organism Homo sapiens
Characteristics Needle core biopsy of the prostate, tumor with Gleason score 8, advanced prostate cancer
Biomaterial provider ATCC
Extracted molecule other
Extraction protocol MicroRNA was isolated from the needle core biopsy 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 -9.5 190 269 283 209 280 322 8 5 0 47 54 28 45 52 27 10 4 0 6.667 11 9.706 4.14 0 0 156 881 -17 69 -19 2 60 9 -50
BUFFER2 100000 182 201 107 207 268 356 1 0 0 41 49 38 41 46 26 9 7 0 -0.75 8.214 5.839 5.884 40.272 0.045 52 264 -25 2 -25 0 -6 8 -50 16.60964047 16.61
BUFFER3 -1.5 189 225 151 186 209 134 19 5 0 37 41 28 39 40 19 3 3 0 19.5 12.667 10.072 4.757 43.509 0.017 156 607 1 41 3 -2 39 2 -50
BUFFER4 6 178 194 109 184 207 131 10 1 0 37 40 12 38 40 11 7 3 0 5 7.125 6.401 4.343 208.726 0.002 156 541 -7 12 2.585 -6 -1 10 2 -50 2.584962501 2.585
BUFFER5 100000 174 215 188 190 223 175 10 3 0 39 41 14 39 41 13 5 1 0 12.5 16 16.045 3.44 0.003 0.001 156 539 -16 27 -16 0 25 2 -50 16.60964047 16.61
BUFFER6 5.4 222 275 270 195 249 241 10 5 0 47 56 36 42 47 20 16 12 0 5.714 10.444 8.415 4.236 5.825 0.508 156 538 32 94 2.433 27 5 80 14 -50 2.432959407 2.433
BUFFER7 5 204 280 362 209 269 258 7 6 0 45 51 22 46 51 21 10 7 0 14.2 11.429 8.49 4.657 252.811 0.003 156 549 -6 76 2.322 -5 -1 71 5 -50 2.321928095 2.322
BUFFER8 -8 206 236 167 198 262 280 4 2 0 45 52 27 46 50 19 10 5 0 6.333 10.5 9.557 3.666 0 0 156 547 7 44 8 -1 38 6 -50
BUFFER9 2.667 215 289 394 207 271 303 7 4 0 48 53 28 45 50 20 8 5 0 10.25 11.167 9.365 3.942 36.549 0.14 156 561 11 90 1.415 8 3 82 8 -50 1.415217825 1.415
BUFFER10 -1 203 275 275 205 253 248 11 5 0 46 51 20 44 51 25 10 3 0 10 5 5.911 4.846 0.002 0 80 339 0 77 -2 2 70 7 -50
BUFFER11 -23 211 360 896 188 262 410 6 3 0 43 49 19 44 48 20 10 6 0 34.4 13.118 11.408 3.653 840.412 0.001 156 589 22 177 23 -1 172 5 -50
BUFFER12 16 200 310 457 184 254 347 8 5 0 44 49 22 43 46 16 13 7 0 21 13.625 10.382 4.142 185.947 0.015 156 534 17 132 4 16 1 126 6 -50 4 4
BUFFER13 3 184 234 249 187 247 288 7 3 0 42 42 8 43 44 12 4 1 0 -47 11.014 9.076 3.789 152.284 0.02 156 608 -4 46 1.585 -3 -1 47 -1 -50 1.584962501 1.585
BUFFER14 -3 183 269 418 189 248 421 5 3 0 45 47 16 43 45 13 6 4 0 20 13.05 11.667 3.767 1228.785 0.001 120 466 -4 84 -6 2 80 4 -50
BUFFER15 100000 203 237 188 185 240 376 4 1 0 44 46 15 44 46 16 5 4 0 26 13.9 11.884 3.019 198.63 0.005 156 630 18 54 18 0 52 2 -50 16.60964047 16.61
BUFFER16 100000 169 217 205 177 230 254 7 3 0 43 44 12 43 44 12 3 2 0 40 11.4 10.631 3.305 0 0 156 587 -8 41 -8 0 40 1 -50 16.60964047 16.61
BUFFER17 3 177 232 236 174 217 240 7 3 0 43 44 9 42 44 13 5 1 0 29 9.25 9.061 3.792 363.825 0.003 156 557 4 60 1.585 3 1 58 2 -50 1.584962501 1.585
BUFFER18 -1 176 277 638 177 222 231 9 3 0 43 49 25 42 44 13 12 7 0 14.286 15.167 10.211 4.383 146.083 0.027 156 612 0 107 -1 1 100 7 -50
BUFFER19 11 190 219 173 179 227 232 7 4 0 43 47 20 42 44 15 9 4 0 8 10.5 9.262 4.222 0.001 0 156 641 12 45 3.459 11 1 40 5 -50 3.459431619 3.459
BUFFER20 -4 182 231 252 178 219 218 8 4 0 42 45 13 43 45 16 4 2 0 26.5 12.5 10.245 3.806 0.001 0 156 683 3 55 4 -1 53 2 -50

Total number of rows: 768

Table truncated, full table size 117 Kbytes.




Supplementary data files not provided
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