|
Status |
Public on May 04, 2006 |
Title |
miRNA expression in newborn Dkk1-expressing transgenic skin sample TG4 versus control littermate skin sample C5 |
Sample type |
other |
|
|
Channel 1 |
Source name |
Dorsal skin dissected from newborn double transgenic K5-rtTA;tetO-Dkk1 mouse TG4
|
Organism |
Mus musculus |
Characteristics |
Strain: K5-rtTA; tetO-Dkk1 treated with doxycycline from day 0.5 of gestation to induce epidermal expression of Dkk1. Strain background: mixed FVB/N, C57BL/6, SJ/L. Age: Newborn. Tissue: Full thickness dorsal skin.
|
Growth protocol |
Treated with doxycycline from day 0.5 of gestation by maintaining the mother on doxycycline-containing chow.
|
Extracted molecule |
other |
Extraction protocol |
Low molecular weight RNA was isolated using the mirVana RNA extraction kit (Ambion).
|
Label |
Cy5
|
Label protocol |
Samples were tagged for labeling using the Ncode miRNA Labeling System (Invitrogen)
|
|
|
Channel 2 |
Source name |
Dorsal skin dissected from control newborn mouse C5
|
Organism |
Mus musculus |
Characteristics |
Strain: Control littermate treated with doxycycline from day 0.5 of gestation to induce epidermal expression of Dkk1. Strain background: mixed FVB/N, C57BL/6, SJ/L. Age: Newborn. Tissue: Full thickness dorsal skin.
|
Growth protocol |
Treated with doxycycline from day 0.5 of gestation by maintaining the mother on doxycycline-containing chow.
|
Extracted molecule |
other |
Extraction protocol |
Low molecular weight RNA was isolated using the mirVana RNA extraction kit (Ambion).
|
Label |
Cy3
|
Label protocol |
Samples were tagged for labeling using the Ncode miRNA Labeling System (Invitrogen)
|
|
|
|
Description |
miRNA expression was compared in skin from control newborn mice and littermate mice ectopically expressing the potent secreted WNT inhibitor Dickkopf 1 (DKK1) in the epidermis, which completely lack hair follicle development. Low molecular weight RNA was isolated using the mirVana RNA extraction kit (Ambion) from full thickness dorsal skin of K5-rtTA; tetO-Dkk1 newborn mice and control littermates following doxycycline treatment from E0.5 to induce expression of Dkk1 in double transgenic epidermis [1]. Control and Dkk1–expressing transgenic samples were tagged for labeling with Cy3 and Cy5 dyes respectively using the Ncode miRNA Labeling System (Invitrogen), mixed by equal mass, and co-hybridized to miRNA arrays that have been described previously [2]. Background-corrected median signals for pixels from each probe spot in both the Cy3 and Cy5 channels were used for analysis. Cy3 (control samples C2, C4, C5) were detected at 532nm and Cy5 (Dkk1–expressing transgenic samples TG1, TG2, TG4) at 635 nm.
References: [1] Wysolmerski, J.J., and Millar, S.E. (2004). Canonical WNT signaling promotes mammary placode development and is essential for initiation of mammary gland morphogenesis. Development 131, 4819-4829.
[2] Mourelatos, Z. (2004). Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 1, 155-161.
|
Data processing |
The log (base 2) transform of the ratio of the background-subtracted medians (635/532) was calculated for each spot.
|
|
|
Submission date |
Apr 25, 2006 |
Last update date |
Apr 26, 2006 |
Contact name |
Sarah E Millar |
E-mail(s) |
sarah.millar@mssm.edu
|
Organization name |
Icahn School of Medicine at Mount Sinai
|
Department |
Developmental, Cell and Regenerative Biology
|
Street address |
Icahn Building, Floor 13 Room 020C, 1425 Madison Ave
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10029 |
Country |
USA |
|
|
Platform ID |
GPL3699 |
Series (1) |
GSE4723 |
Comparison of miRNA expression in Dickkopf1-expressing versus control newborn mouse skin |
|
Data table header descriptions |
ID_REF |
|
VALUE |
Log2 Ratio (transgenic/control; 635/532); log (base 2) transformation of the ratio of the background-corrected medians |
X |
the X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image |
Y |
the Y-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image |
Dia. |
the diameter in µm of the feature-indicator |
F635 Median |
median feature pixel intensity at wavelength #1 (635 nm) |
F635 Mean |
mean feature pixel intensity at wavelength #1 (635 nm) |
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 |
the mean feature background intensity at wavelength #2 (532 nm) |
B532 SD |
the standard deviation of the feature background 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 Medians (635/532) |
the ratio of the median intensities of each feature for each wavelength, with the median background subtracted |
Ratio of Means |
the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted |
Median of Ratios (635/532) |
the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted |
Mean of Ratios (635/532) |
the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted |
Ratios SD (635/532) |
the geometric standard deviation of the pixel intensity ratios |
Rgn Ratio (635/532) |
the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature |
Rgn R2 (635/532) |
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 (635/532) |
the sum of the median intensities for each wavelength, with the median background subtracted |
Sum of Means (635/532) |
the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted |
F635 Median - B635 |
the median feature pixel intensity at 635nm with the median background subtracted |
F532 Median - B532 |
the median feature pixel intensity at 532nm with the median background subtracted |
F635 Mean - B635 |
the mean feature pixel intensity at 635nm with the median background subtracted |
F532 Mean - B532 |
the mean feature pixel intensity at wavelength 532nm with the median background subtracted |
F635 Total Intensity |
the total feature pixel intensity at 635nm |
F532 Total Intensity |
the total feature pixel intensity at 532nm |
SNR 635 |
the signal-to-noise ratio at 635nm, defined by (Mean Foreground 635nm - Mean Background 635nm) / (Standard deviation of Background 635nm) |
SNR 532 |
the signal-to-noise ratio at 532nm, defined by (Mean Foreground 532nm - Mean Background 532nm) / (Standard deviation of Background 532nm) |
Flags |
the type of flag associated with a feature |
UNF_VALUE |
Log Ratio (635/532); log (base 2) transform of the ratio of the background-corrected medians |