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Sample GSM87299 Query DataSets for GSM87299
Status Public on Feb 01, 2006
Title Controlvs.treated_LAQ-824_5hrs_rep4
Sample type mixed
 
Channel 1
Source name Untreated SKBr3 cells
Organism Homo sapiens
Characteristics Untreated SKBr3 breast cancer cell line
Biomaterial provider ATCC
Treatment protocol Control cells were not treated.
Growth protocol Standard growth conditions.
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 Treated SKBr3 cells
Organism Homo sapiens
Characteristics SKBr3 breast cancer cell line treated with LAQ-824, a histone deacetylase inhibitor
Biomaterial provider ATCC
Treatment protocol SKBr3 cells were treated with 20 uM LAQ-824 for 5 hours
Growth protocol Standard growth conditions
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 09, 2005
Last update date Jan 04, 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)
GSE3798 Rapid alteration of microRNA levels by histone deacetylase inhibition

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_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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -50
BUFFER2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -50
BUFFER3 100000 186 200 100 182 194 100 26 4 0 41 61 78 41 56 64 6 6 0 0.9 9 4.891 4.891 3.053 0.002 50 265 4 38 4 0 18 20 -50 16.61
BUFFER4 -8.5 194 208 104 177 193 100 19 6 0 39 55 50 41 53 57 10 5 0 2.214 6.528 5.128 5.038 64.895 0 156 597 15 45 17 -2 31 14 -50
BUFFER5 4.333 188 212 129 201 237 178 5 0 0 43 92 166 46 83 97 12 6 0 0.239 6.243 3.984 5.23 3.405 0.032 156 611 -16 57 -13 -3 11 46 -50 2.115
BUFFER6 -1 236 265 157 232 274 201 11 2 0 85 157 138 89 149 154 20 7 0 0.485 1.756 1.498 4.451 10.046 0.01 156 582 0 101 4 -4 33 68 -50
BUFFER7 -0.095 237 269 199 239 274 197 12 3 0 115 161 126 94 163 156 21 4 0 0.448 1.832 1.292 4.387 7.141 0.018 156 611 19 97 -2 21 30 67 -50
BUFFER8 -3.667 260 295 154 249 288 218 13 1 0 91 160 131 94 168 169 19 3 0 0.697 1.386 1.154 3.793 31.058 0.001 156 611 8 112 11 -3 46 66 -50
BUFFER9 0.5 247 293 273 251 308 250 5 1 0 92 152 143 100 177 202 10 2 0 0.808 2.068 1.756 4.097 1.974 0.056 156 582 -12 94 -4 -8 42 52 -50 -1
BUFFER10 0.462 251 285 174 245 295 217 15 3 0 108 169 149 95 172 167 17 7 0 0.541 1.786 1.501 4.422 10.268 0.005 156 611 19 114 6 13 40 74 -50 -1.115
BUFFER11 3 230 263 158 242 275 167 14 3 0 86 145 134 90 158 157 17 4 0 0.382 2.043 2.111 4.384 16.227 0.001 156 611 -16 76 -12 -4 21 55 -50 1.585
BUFFER12 1.25 219 273 281 239 271 237 8 2 0 90 144 116 106 158 142 16 4 0 0.895 1.78 1.403 3.636 0.034 0.003 156 582 -36 72 -20 -16 34 38 -50 0.322
BUFFER13 0.833 246 274 164 231 267 245 9 2 0 118 198 200 100 151 128 26 15 0 0.439 1.03 1.112 3.864 34.968 0.001 156 582 33 141 15 18 43 98 -50 -0.263
BUFFER14 -2.667 253 281 186 245 278 167 14 3 0 99 149 118 102 160 142 18 3 0 0.766 1.63 1.345 4.143 17.141 0.001 156 611 5 83 8 -3 36 47 -50
BUFFER15 -0.182 237 285 180 239 294 317 7 1 0 119 162 130 108 158 136 16 5 0 0.852 2.039 1.53 4.112 171.738 0 156 646 9 100 -2 11 46 54 -50
BUFFER16 -1.818 261 278 141 241 296 308 3 0 0 99 151 125 110 161 129 17 5 0 0.902 1.052 0.888 4.084 0.003 0 156 667 9 78 20 -11 37 41 -50
BUFFER17 2.4 272 290 154 248 280 162 16 5 0 103 163 145 93 154 137 23 8 0 0.6 1.611 1.457 4.338 0.097 0.001 156 659 34 112 24 10 42 70 -50 1.263
BUFFER18 4 300 344 200 244 278 175 27 14 0 108 184 167 94 157 140 27 12 0 1.111 1.34 1.423 5.136 3.209 0.002 156 611 70 190 56 14 100 90 -50 2
BUFFER19 14.5 221 248 154 250 288 211 7 1 0 103 173 159 105 165 146 23 6 0 -0.029 1.92 1.458 4.175 15.367 0.003 156 582 -31 66 -29 -2 -2 68 -50 3.858
BUFFER20 -1.5 248 290 201 266 310 235 10 5 0 114 183 158 102 170 156 25 10 0 0.296 2.044 1.637 4.786 0.01 0 156 611 -6 105 -18 12 24 81 -50

Total number of rows: 768

Table truncated, full table size 111 Kbytes.




Supplementary data files not provided

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