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Sample GSM106586 Query DataSets for GSM106586
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

Data table
ID_REF VALUE X Y Dia. 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 Medians (635/532) Ratio of Means Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) F Pixels B Pixels Sum of Medians (635/532) Sum of Means (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags UNF_VALUE
10101 -5.885 2170 7960 140 1188 1305 743 81 87 40 98 96 0 65535 53668 20120 131 136 47 100 100 67 0.017 0.023 0.022 0.02 2.214 0.022 0.735 156 1020 66511 54761 1107 65404 1224 53537 203522 8372130 30.45 1138.979 0 -5.885
10201 -5.742 2410 7960 150 1305 1416 779 83 90 42 98 97 0 65535 56096 17960 133 138 47 100 100 71 0.019 0.024 0.023 0.02 2.097 0.023 0.744 156 1084 66624 57296 1222 65402 1333 55963 220959 8751051 31.571 1190.596 0 -5.742
10301 -5.697 2670 7960 150 1345 1419 773 84 91 43 98 97 0 65535 54982 19020 136 142 50 100 100 70 0.019 0.024 0.025 0.022 1.994 0.023 0.735 156 1084 66660 56181 1261 65399 1335 54846 221382 8577173 30.884 1096.8 0 -5.697
10401 -5.571 2910 7960 150 1462 1484 720 86 91 38 100 100 0 65535 56835 16841 140 144 52 100 100 71 0.021 0.025 0.024 0.023 1.69 0.023 0.764 156 1068 66771 58093 1376 65395 1398 56695 231512 8866306 36.658 1090.212 0 -5.571
10501 -5.453 3160 7960 150 1576 1664 663 83 91 42 100 100 0 65535 57985 15807 141 144 49 100 100 75 0.023 0.027 0.026 0.026 1.675 0.025 0.78 156 1090 66887 59425 1493 65394 1581 57844 259591 9045662 37.452 1180.429 0 -5.453
10601 -5.39 3410 7960 150 1642 1677 812 82 90 44 99 99 0 65535 57680 15937 139 144 50 100 100 75 0.024 0.028 0.028 0.025 1.897 0.026 0.748 156 967 66956 59136 1560 65396 1595 57541 261584 8998103 36.068 1150.72 0 -5.39
10701 -5.643 3650 7960 160 1391 1386 889 82 90 45 89 87 0 65535 50378 21922 139 144 51 100 99 60 0.02 0.026 0.026 0.021 2.311 0.026 0.774 208 918 66705 51543 1309 65396 1304 50239 288212 10478687 28.8 984.98 0 -5.643
10801 -5.513 3910 7960 160 1516 1542 918 84 92 44 95 92 0 65535 52276 20288 139 144 49 100 100 60 0.022 0.028 0.029 0.023 2.525 0.028 0.77 208 1101 66828 53595 1432 65396 1458 52137 320836 10873379 32.955 1063.918 0 -5.513
10901 -5.401 4150 7960 150 1636 1698 746 88 94 47 99 99 0 65535 56484 16658 139 146 57 100 100 70 0.024 0.029 0.027 0.027 1.732 0.027 0.766 156 1026 66944 57955 1548 65396 1610 56345 264842 8811427 34.128 988.386 0 -5.401
11001 -5.6 4400 7960 160 1435 1464 905 87 94 46 91 89 0 65535 51302 20832 138 146 63 100 100 60 0.021 0.027 0.028 0.022 2.634 0.027 0.771 208 1200 66745 52541 1348 65397 1377 51164 304531 10670733 29.783 812 0 -5.6
11101 -5.505 4650 7960 160 1526 1528 990 86 93 45 91 89 0 65535 49758 22132 142 145 48 100 100 57 0.022 0.029 0.029 0.024 2.365 0.029 0.78 208 1218 66833 51058 1440 65393 1442 49616 317873 10349560 31.889 1033.604 0 -5.505
11201 -5.123 4910 7960 150 1964 2026 795 87 95 45 100 100 0 65535 56906 15846 142 148 50 100 100 73 0.029 0.034 0.032 0.033 1.433 0.03 0.759 156 1042 67270 58703 1877 65393 1939 56764 315979 8877318 42.911 1135.16 0 -5.123
11301 -5.463 5150 7960 160 1566 1631 1082 83 91 40 93 89 0 65535 50264 21980 139 143 46 100 100 59 0.023 0.031 0.031 0.024 2.618 0.031 0.77 208 1182 66879 51673 1483 65396 1548 50125 339156 10455008 38.5 1089.587 0 -5.463
11401 -5.346 5400 7960 160 1694 1674 1017 86 93 46 91 88 0 65535 51855 20150 140 151 160 100 99 58 0.025 0.031 0.031 0.024 2.664 0.03 0.762 208 1176 67003 53303 1608 65395 1588 51715 348229 10785938 34.37 323.15 0 -5.346
11501 -5.299 5650 7960 160 1749 1793 1090 88 97 51 94 91 0 65535 51717 20137 145 156 159 100 100 60 0.025 0.033 0.032 0.027 2.075 0.033 0.787 208 1225 67051 53277 1661 65390 1705 51572 373043 10757123 33.255 324.283 0 -5.299
11601 -5.141 5900 7950 150 1939 1985 954 86 95 46 99 98 0 65535 57405 14318 147 193 878 100 100 69 0.028 0.033 0.034 0.029 2.046 0.033 0.748 156 1184 67241 59157 1853 65388 1899 57258 309696 8955117 41.087 65.162 0 -5.141
10102 1.048 2160 8210 140 258 299 200 76 84 39 84 73 0 208 230 92 120 127 50 72 41 0 2.068 2.027 1.944 1.68 4.175 3.471 0.177 156 998 270 333 182 88 223 110 46650 35880 5.513 2.06 0 1.048
10202 1.144 2410 8220 150 297 340 206 76 85 42 90 78 0 222 235 104 122 128 49 70 50 0 2.21 2.336 2.159 2.103 4.18 3.279 0.242 156 1017 321 377 221 100 264 113 53063 36700 6.071 2.184 0 1.144
10302 -1.084 2660 8210 130 2808 3062 1355 81 89 43 100 100 0 5905 6463 2733 126 130 47 100 100 0 0.472 0.47 0.466 0.464 1.454 0.457 0.878 120 856 8506 9318 2727 5779 2981 6337 367418 775505 69.14 134.745 0 -1.084
10402 -0.839 2910 8210 130 7947 8130 2876 82 88 40 100 100 0 14198 14981 4965 129 133 52 100 100 0 0.559 0.542 0.537 0.537 1.26 0.543 0.934 120 868 21934 22900 7865 14069 8048 14852 975604 1797761 201.05 285.538 0 -0.839

Total number of rows: 4608

Table truncated, full table size 886 Kbytes.




Supplementary file Size Download File type/resource
GSM106586.gpr.gz 391.1 Kb (ftp)(http) GPR

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