|
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.
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|
|
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. |