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Sample GSM148494 Query DataSets for GSM148494
Status Public on Jan 11, 2009
Title Normal prostate vs. 24858T (prostate tumor)
Sample type other
 
Channel 1
Source name Normal prostate
Organism Homo sapiens
Characteristics Normal prostate reference control. RNA was isolated from prostate tissue from a 70 year old male without prostate cancer. RNA was enriched for the microRNA fraction.
Biomaterial provider Ambion
Treatment protocol NA
Growth protocol NA
Extracted molecule other
Extraction protocol MicroRNA was isolated from the untreated SKBr3 cells 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 24858T (prostate tumor)
Organism Homo sapiens
Characteristics Prostate tumor. RNA was isolated from a radical prostatectomy specimen 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 untreated SKBr3 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.
 
 
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 Dec 06, 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 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 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 -5.333 161 352 821 177 313 1108 3 2 0 49 61 69 46 52 22 14 8 0 11.667 11.909 11.412 3.564 26.58 0.288 156 881 -13 190 -16 3 175 15 -50
BUFFER2 17 202 254 218 168 298 619 5 0 0 48 52 17 46 51 18 15 7 0 14.333 11.527 7.628 4.477 1905.941 0 52 264 36 92 4.087 34 2 86 6 -50 4.087
BUFFER3 100000 187 255 275 166 286 611 5 1 0 46 53 22 46 54 79 1 0 0 12.714 8.045 6.124 4.662 204.487 0.007 156 607 21 96 16.61 21 0 89 7 -50 16.61
BUFFER4 100000 161 403 1637 158 238 676 4 2 0 45 59 88 45 50 43 4 2 0 17.5 9.9 8.85 3.287 17.053 0.067 156 541 3 259 16.61 3 0 245 14 -50 16.61
BUFFER5 25.5 208 314 356 157 223 466 9 3 0 46 51 19 44 48 31 9 2 0 22.429 10.592 9.448 3.741 247.131 0.004 156 539 53 164 4.672 51 2 157 7 -50 4.672
BUFFER6 1 158 403 925 157 246 570 8 5 0 44 60 108 43 48 36 7 3 0 14.471 8.786 7.842 3.577 15.797 0.478 156 538 2 263 0 1 1 246 17 -50 0
BUFFER7 -10 153 511 1273 163 269 599 8 7 0 43 61 72 42 48 37 13 5 0 18.316 10.75 8.205 4.461 38.563 0.37 156 549 -9 367 -10 1 348 19 -50
BUFFER8 -6.5 148 288 584 161 292 1094 3 0 0 45 52 39 43 47 21 13 5 0 14.111 11 11.113 3.179 128.431 0.048 156 547 -11 136 -13 2 127 9 -50
BUFFER9 100000 156 250 393 162 327 1041 1 0 0 43 50 28 43 48 22 9 7 0 12.571 9.333 8.252 3.785 285.818 0.015 156 561 -6 95 16.61 -6 0 88 7 -50 16.61
BUFFER10 -0.5 162 308 697 163 589 3106 1 0 0 45 56 39 43 54 91 2 1 0 11.154 6.611 6.658 4.391 66.05 0.337 80 339 1 158 -1 2 145 13 -50
BUFFER11 -21 140 209 342 161 472 2476 0 0 0 43 53 42 42 50 71 3 2 0 4.364 12.6 10.166 3.269 3650.907 0 156 589 -20 59 -21 1 48 11 -50
BUFFER12 -4 169 548 2300 173 396 1280 4 2 0 43 61 142 42 47 31 12 4 0 19.737 11.8 9.017 4.591 33.877 0.369 156 534 -3 394 -4 1 375 19 -50
BUFFER13 -2 163 495 1436 169 412 1783 3 3 0 44 68 131 41 50 97 4 2 0 12.074 11.417 10.441 3.546 20.044 0.629 156 608 -3 353 -6 3 326 27 -50
BUFFER14 4 164 676 2567 160 373 1823 5 2 0 43 62 113 42 55 116 3 0 0 25.8 11.699 10.283 4.335 34.324 0.318 120 466 5 536 2 4 1 516 20 -50 2
BUFFER15 31 182 318 461 151 277 617 8 4 0 43 48 23 42 48 41 6 1 0 27.833 12.188 9.653 3.62 32.036 0.541 156 630 32 173 4.954 31 1 167 6 -50 4.954
BUFFER16 4.75 183 338 546 164 369 1126 5 2 0 45 54 27 41 48 42 10 3 0 13.385 9.5 9.245 4.161 31.328 0.272 156 587 23 187 2.248 19 4 174 13 -50 2.248
BUFFER17 -4.5 171 341 1018 180 412 1185 2 1 0 43 56 72 41 48 41 10 3 0 10.733 9.875 8.103 4.568 27.956 0.426 156 557 -7 176 -9 2 161 15 -50
BUFFER18 -22 143 225 437 165 414 2025 1 0 0 42 50 35 41 51 93 2 1 0 6.667 11.167 10.677 3.177 38.826 0.483 156 612 -21 69 -22 1 60 9 -50
BUFFER19 2 176 948 3662 172 478 2063 4 3 0 43 243 1516 41 54 96 5 5 0 3.842 10.619 8.738 4.139 4.254 0.484 156 641 6 978 1 4 2 776 202 -50 1
BUFFER20 4 175 367 824 167 498 1614 3 1 0 43 54 46 41 50 67 5 2 0 15.385 12.75 8.995 4.841 59.531 0.105 156 683 10 213 2 8 2 200 13 -50 2

Total number of rows: 768

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM148494.gpr.gz 45.7 Kb (ftp)(http) GPR

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