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Sample GSM566781 Query DataSets for GSM566781
Status Public on Jul 21, 2011
Title Gene expression profiling of type 1 single fiber of mouse skeletal muscle (Soleus 6)
Sample type RNA
 
Channel 1
Source name EDL and soleus whole muscles mixture (reference)
Organism Mus musculus
Characteristics tissue: 3 pairs of EDL and soleus whole muscle pooled from 3 wild-type CD1 mice
myofiber type: balanced composition of type 1 and type 2B myofibres
Biomaterial provider Departement of Biology - University of Padova, Italy
Extracted molecule total RNA
Extraction protocol Total RNA was purified from muscles following the standard Trizol protocol. The Nanodrop ND-1000 (Celbio) was used for RNA quantification and RNA 6000 Nano LabChip kit (Agilent Technologies) was used for RNA quality control in conjunction with an Agilent Bioanalyzer 2001.
Label Cy3
Label protocol Two rounds of linear amplification of mRNA from 100ng of total RNA was carried on using the Amino Allyl Message-Amp-aRNA kit (Ambion) according to the manufacturer’s recommendations. 5μg of aRNA from the sample was coupled to Cy3 dye (Amersham Pharmacia Biotech) to obtain labeled aRNA ready for microarray hybridization.
 
Channel 2
Source name Type 1 single myofibre isolated by enzymatic digestion (test)
Organism Mus musculus
Characteristics tissue: Soleus whole muscle
myofiber type: type 1
Biomaterial provider Departement of Biology - University of Padova, Italy
Extracted molecule total RNA
Extraction protocol Total RNA was purified from the major part of fibre following the standard RNeasy Micro Kit (Qiagen) protocol.
Label Cy5
Label protocol Two rounds of linear amplification of mRNA from the total RNA extracted was carried on using the Amino Allyl Message-Amp-aRNA kit (Ambion) according to the manufacturer’s recommendations. 5μg of aRNA from the sample was coupled to Cy5 dye (Amersham Pharmacia Biotech) to obtain labeled aRNA ready for microarray hybridization.
 
 
Hybridization protocol Labeled RNAs were concentrated by ethanol precipitation and dissolved in 118μl of hybridization buffer (5XSSC, 0.1% SDS, 25% formamide). Labeled aRNA target from single fibre sample and whole muscle control were mixed before precipitation. After denaturation at 90°C for 2 min, the labeled targets were added to the microarrays, previously incubated in prehybridization buffer (5X SSC, 0.1% SDS,100ng/ul ss-DNA, 5X Denhardt) for ~ 20 hours at 46°C. Hybridization was carried for 44 hours at 46°C in an ArrayBooster microarray incubator (Advalytix), followed by a series of post-hybridization washings.
Scan protocol Fluorescence detection was carried out on a VersArray ChipReader dual confocal laser scanner (Bio-Rad) at 6µm resolution, and raw scanner images were analyzed with QuantArray software (Perkin-Elmer).
Description We compared the transcription profiles of a type 1 isolated myofibre by microarray competitive hybridization against a pool of soleus and EDL whole muscles.
Data processing Normalization of the expression levels was performed with MIDAW tool (Romualdi et al., 2005 - Nucleic Acids Res. 33: W644-9).
 
Submission date Jul 15, 2010
Last update date Jul 21, 2011
Contact name Gerolamo Lanfranchi
E-mail(s) [email protected]
Phone +39-0498276219
Organization name University of Padova
Department CRIBI - Biotechnology Center and Biology Department
Lab Functional Genomics Lab
Street address Via U. Bassi, 58/B
City Padova
ZIP/Postal code 35131
Country Italy
 
Platform ID GPL10688
Series (1)
GSE23244 Microgenomic Analysis in Skeletal Muscle: Expression Signatures of Individual Fast and Slow Myofibers

Data table header descriptions
ID_REF
VALUE Log(2) ratio of intensities normalized by global mean normalization by MIDAW software (Romualdi et al. 2005) , defined as Channel 2 divided by Channel 1 (test/reference) (data used in our work)
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
Diameter the diameter in μm of the feature-indicator
F Pixels the total number of feature pixels
B Pixels the total number of background pixels
Footprint This is the distance between the expected position of a spot and its actual position
Flags the type of flag associated with a feature
Ch1 Median median feature pixel intensity at wavelength #1 (633 nm)
Ch1 Mean mean feature pixel intensity at wavelength #1 (633 nm)
Ch1 SD the standard deviation of the feature pixel intensity at wavelength #1 (633 nm)
Ch1 B Median the median feature background intensity at wavelength #1 (633 nm)
Ch1 B Mean the mean feature background intensity at wavelength #1 (633 nm)
Ch1 B SD the standard deviation of the feature background intensity at wavelength #1 (633 nm)
Ch1 % > B + 1 SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (633 nm)
Ch1 % > B + 2 SD the percentage of feature pixels with intensities more than two standard deviation above the background pixel intensity, at wavelength #1 (633 nm)
Ch1 F % Sat. the percentage of feature pixels at wavelength #1 (633 nm) that are saturated
Ch1 Median - B the median feature pixel intensity at wavelength #1 (633 nm) with the median background subtracted
Ch1 Mean - B the mean feature pixel intensity at wavelength #1 (633 nm) with the median background subtracted
Ch1 SignalNoiseRatio the signal-to-noise ratio at wavelength #1 (633 nm), defined by (Mean Foreground 1- Mean Background 1) / (Standard deviation of Background 1)
Ch2 Median median feature pixel intensity at wavelength #2 (543 nm)
Ch2 Mean mean feature pixel intensity at wavelength #2 (543 nm)
Ch2 SD the standard deviation of the feature pixel intensity at wavelength #2 (543 nm)
Ch2 B Median the median feature background intensity at wavelength #2 (543 nm)
Ch2 B Mean the mean feature background intensity at wavelength #2 (543 nm)
Ch2 B SD the standard deviation of the feature background intensity at wavelength #2 (543 nm)
Ch2 % > B + 1 SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (543 nm)
Ch2 % > B + 2 SD the percentage of feature pixels with intensities more than two standard deviation above the background pixel intensity, at wavelength #2 (543 nm)
Ch2 F % Sat. the percentage of feature pixels at wavelength #2 (543 nm) that are saturated
Ch2 Median - B the median feature pixel intensity at wavelength #2 (543 nm) with the median background subtracted
Ch2 Mean - B the mean feature pixel intensity at wavelength #2 (543 nm) with the median background subtracted
Ch2 SignalNoiseRatio the signal-to-noise ratio at wavelength #2 (543 nm), defined by (Mean Foreground 2- Mean Background 2) / (Standard deviation of Background 2)
Ch2 Ratio of Medians the ratio of the median intensities of each featurefor each wavelength, with the median background subtracted
Ch2 Ratio of Means the ratio of the arithmetic mean intensities of each featurefor each wavelength, with the median background subtracted
Ch2 Median of Ratios the median of pixel-by-pixel ratios of pixel intensitiesfor each wavelength, with the median background subtracted
Ch2 Mean of Ratios the mean of pixel-by-pixel ratios of pixel intensitiesfor each wavelength, with the median background subtracted
Ch2 Ratios SD the standard deviation of pixel intensity ratios
Ch2 Rgn Ratio the regression ratio
Ch2 Rgn R²
Ch2 Log Ratio log (base 2) transform of the ratio of the medians
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
Ch1 N Median median feature pixel intensity at wavelength #1 (633 nm) normalized with ScanArray Total method (data not used in our work)
Ch1 N Mean the mean feature background intensity at wavelength #1 (633 nm) normalized with ScanArray Total method (data not used in our work)
Ch1 N (Median-B) the median feature pixel intensity at wavelength #1 (633 nm) with the median background subtracted normalized with ScanArray Total method (data not used in our work)
Ch1 N (Mean-B) the mean feature pixel intensity at wavelength #1 (633 nm) with the median background subtracted normalized with ScanArray Total method (data not used in our work)
Ch2 N Median median feature pixel intensity at wavelength # (543 nm)2 normalized with ScanArray Total method (data not used in our work)
Ch2 N Mean the mean feature background intensity at wavelength #2 (543 nm) normalized with ScanArray Total method (data not used in our work)
Ch2 N (Median-B) the median feature pixel intensity at wavelength #2 (543 nm) with the median background subtracted normalized with ScanArray Total method (data not used in our work)
Ch2 N (Mean-B) the mean feature pixel intensity at wavelength #2 (543 nm) with the median background subtracted normalized with ScanArray Total method (data not used in our work)
Ch2 N Ratio of Medians the ratio of the normalized (with ScanArray Total method) median intensities of each feature for each wavelength, with the median background subtracted (data not used in our work)
Ch2 N Ratio of Means the ratio of the normalized (with ScanArray Total method) arithmetic mean intensities of each feature for each wavelength, with the median background subtracted (data not used in our work)
Ch2 N Median of Ratios the normalized (with ScanArray Total method) median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted (data not used in our work)
Ch2 N Mean of Ratios the normalized (with ScanArray Total method) mean of pixel-by-pixel ratios of pixel intensities, with the median background subtracted (data not used in our work)
Ch2 N Rgn Ratio the regression ratio of normalized (with ScanArray Total method) data (data not used in our work)
Ch2 N Log Ratio log (base 2) transform of the ratio of the normalized (with ScanArray Total method) medians data (data not used in our work)

Data table
ID_REF VALUE X Y Diameter F Pixels B Pixels Footprint Flags Ch1 Median Ch1 Mean Ch1 SD Ch1 B Median Ch1 B Mean Ch1 B SD Ch1 % > B + 1 SD Ch1 % > B + 2 SD Ch1 F % Sat. Ch1 Median - B Ch1 Mean - B Ch1 SignalNoiseRatio Ch2 Median Ch2 Mean Ch2 SD Ch2 B Median Ch2 B Mean Ch2 B SD Ch2 % > B + 1 SD Ch2 % > B + 2 SD Ch2 F % Sat. Ch2 Median - B Ch2 Mean - B Ch2 SignalNoiseRatio Ch2 Ratio of Medians Ch2 Ratio of Means Ch2 Median of Ratios Ch2 Mean of Ratios Ch2 Ratios SD Ch2 Rgn Ratio Ch2 Rgn R² Ch2 Log Ratio Sum of Medians Sum of Means Ch1 N Median Ch1 N Mean Ch1 N (Median-B) Ch1 N (Mean-B) Ch2 N Median Ch2 N Mean Ch2 N (Median-B) Ch2 N (Mean-B) Ch2 N Ratio of Medians Ch2 N Ratio of Means Ch2 N Median of Ratios Ch2 N Mean of Ratios Ch2 N Rgn Ratio Ch2 N Log Ratio
1 0.909926525 941 6876 54 47 398 7 3 1861 1756 512.33 250 248 52.3 100 100 0 1611 1506 35.59 6857 6643 1576.63 715 716 84.96 100 100 0 6142 5928 80.71 3.81 3.94 3.82 4.27 1.77 2.63 0.73 1.931 7753 7434 1861 1756 1611 1506 3378 3273 3026 2921 1.88 1.94 1.88 2.1 1.3 0.909
2 0.656678906 1100 6869 48 41 466 4 3 2139 1952 499.36 232 234 49.94 100 100 0 1907 1720 42.83 6811 6573 1359.94 711 719 84.82 100 100 0 6100 5862 80.3 3.2 3.41 3.35 3.64 1.27 2.37 0.76 1.678 8007 7582 2139 1952 1907 1720 3356 3238 3005 2888 1.58 1.68 1.65 1.79 1.17 0.656
3 0.82009749 1263 6870 54 48 375 6 3 1916 1792 550.19 235 242 53.95 100 100 0 1681 1557 35.52 6736 6134 1534.37 714 718 82.63 100 100 0 6022 5420 81.52 3.58 3.48 3.43 3.7 1.06 2.5 0.8 1.841 7703 6977 1916 1792 1681 1557 3319 3022 2967 2670 1.76 1.72 1.69 1.83 1.23 0.82
4 0.961413313 1425 6870 48 40 443 8 3 1884 1840 404.6 229 231 45.75 100 100 0 1655 1611 41.18 7253 6980 1003.41 714 721 91.77 100 100 0 6539 6266 79.04 3.95 3.89 3.92 4.08 0.94 2.22 0.8 1.982 8194 7877 1884 1840 1655 1611 3573 3439 3222 3087 1.95 1.92 1.93 2.01 1.1 0.961
5 0.910461757 3984 6876 42 27 443 5 3 248 235 62.01 205 208 39.78 51.9 14.8 0 43 30 6.23 874 961 162.49 710 702 79.44 88.9 51.9 0 164 251 11 3.81 8.37 5.52 6.71 3.16 1.94 0.55 1.931 207 281 248 235 43 30 431 473 81 124 1.88 4.12 2.72 3.3 0.96 0.91
6 -0.020825493 4137 6873 85 136 288 6 1 216 220 45.8 206 207 44.76 23.5 7.4 0 10 14 4.83 718 719 78.13 698 694 73.22 31.6 5.9 0 20 21 9.81 2 1.5 1.92 2.57 2.11 1.27 0.56 1 30 35 216 220 10 14 354 355 10 10 0.99 0.74 0.95 1.27 0.63 -0.019
7 1.287296802 4302 6880 66 78 375 10 3 212 226 51.06 191 195 47.66 35.9 17.9 0 21 35 4.45 794 801 95.3 690 695 81.04 64.1 42.3 0 104 111 9.8 4.95 3.17 3.64 5.62 6 1.42 0.58 2.308 125 146 212 226 21 35 391 395 51 55 2.44 1.56 1.79 2.77 0.7 1.287
8 -1.020825493 4464 6872 85 135 311 1 1 207 204 34.43 214 208 48.7 5.9 0 0 -6 -9 4.25 671 677 73.78 693 699 86.63 9.6 1.5 0 -21 -15 7.75 3.14 1.6 3.24 12.59 22.41 1.27 0.35 1.652 -29 -26 207 204 -6 -9 331 334 -10 -7 1.55 0.79 1.6 6.21 0.63 0.633
9 1.038068196 4625 6864 85 139 311 6 1 199 197 40.83 193 200 43.14 16.5 2.2 0 6 4 4.61 738 754 113.05 713 717 82.26 28.1 13.7 0 25 41 8.97 4.17 10.25 3.7 4.13 2.76 2.13 0.59 2.059 31 45 199 197 6 4 364 372 12 20 2.06 5.06 1.82 2.04 1.05 1.04
10 2.22710202 4772 6880 85 136 288 15 1 191 203 40.25 185 188 44.05 25 6.6 0 6 18 4.34 747 750 75.09 690 707 84.81 30.9 8.8 0 57 60 8.81 9.5 3.33 3.07 7.25 8.65 1.33 0.51 3.248 63 78 191 203 6 18 369 370 28 30 4.69 1.65 1.52 3.58 0.66 2.229
11 3.679614225 4938 6867 85 135 311 7 1 178 186 42.46 181 183 40 17 7.4 0 -2 5 4.45 718 727 77.67 692 689 84.1 24.4 5.2 0 26 35 8.54 -8.67 7 4 12.73 21.12 1.29 0.49 0 23 40 178 186 -2 5 354 359 13 17 -4.28 3.45 1.97 6.28 0.63 -1.019
12 0.622811258 945 7026 48 40 443 9 3 2376 2272 466.93 272 275 49.01 100 100 0 2104 2000 48.48 7288 7298 1128.78 714 718 84.1 100 100 0 6574 6584 86.66 3.12 3.29 3.24 3.44 0.86 1.92 0.63 1.644 8678 8584 2376 2272 2104 2000 3591 3595 3239 3244 1.54 1.62 1.6 1.69 0.94 0.622
13 -0.550761382 1102 7033 54 52 375 8 3 4958 5095 1458.85 251 254 49.2 100 100 0 4707 4844 100.77 7226 7435 1889.63 706 701 85.26 100 100 0 6520 6729 84.75 1.39 1.39 1.38 1.42 0.25 1.18 0.83 0.47 11227 11573 4958 5095 4707 4844 3560 3663 3212 3315 0.68 0.68 0.68 0.7 0.58 -0.551
14 1.346777063 1271 7025 60 65 375 14 3 2777 2689 746.79 265 263 49.52 100 100 0 2512 2424 56.07 13685 13288 4338.62 721 721 76.18 100 100 0 12964 12567 179.64 5.16 5.18 5.25 5.45 2.13 4.98 0.74 2.368 15476 14991 2777 2689 2512 2424 6742 6547 6387 6191 2.54 2.55 2.59 2.68 2.45 1.346
15 0.729765364 1428 7032 66 75 398 12 3 655 602 123.68 244 249 50.53 100 96 0 411 358 12.96 2093 2032 420.43 710 709 74.87 100 97.3 0 1383 1322 27.96 3.36 3.69 3.62 3.8 1.14 3.08 0.82 1.751 1794 1680 655 602 411 358 1031 1001 681 651 1.66 1.82 1.78 1.87 1.52 0.729
16 0.850108224 1588 7031 60 66 375 11 3 1538 1522 359.8 238 249 52.26 100 100 0 1300 1284 29.43 5463 5189 972.07 708 710 68.83 100 100 0 4755 4481 79.37 3.66 3.49 3.42 3.66 0.85 2.25 0.69 1.871 6055 5765 1538 1522 1300 1284 2691 2556 2343 2208 1.8 1.72 1.69 1.8 1.11 0.85
17 -1.020825493 1729 7035 85 136 311 10 1 219 229 44.7 232 237 47.95 16.2 0.7 0 -12 -2 4.57 711 709 72.13 714 723 88.2 13.2 1.5 0 -2 -4 8.06 0.23 1.67 1.5 2.27 2.95 1.17 0.53 -2.115 -16 -8 219 229 -12 -2 351 350 0 -1 0.11 0.82 0.74 1.12 0.58 -3.134
18 -4.828180415 1892 7028 85 137 288 4 1 250 251 44.09 236 246 41.76 24.1 6.6 0 14 15 5.99 701 708 78.56 726 712 87.53 9.5 0.7 0 -24 -17 8.01 -1.79 -1.2 1.09 1.26 0.95 1.25 0.49 0 -11 -3 250 251 14 15 346 349 -11 -8 -0.88 -0.59 0.54 0.62 0.62 -1.019
19 0.452410908 2072 7036 66 78 352 16 3 23585 21776 8362.97 240 244 49.39 100 100 0 23345 21536 477.51 65535 62127 10219.59 719 725 93.52 100 100 50 64816 61408 700.79 2.78 2.85 2.75 4.93 9.64 0.72 0.35 1.473 88161 82944 23585 21776 23345 21536 32287 30608 31933 30254 1.37 1.4 1.36 2.43 0.36 0.452
20 0.549779019 2240 7038 66 79 352 24 3 2017 1788 627.05 233 237 45.45 100 97.5 0 1784 1555 44.38 5997 5556 1647.49 698 703 74.49 100 100 0 5299 4858 80.51 2.97 3.12 3.09 3.66 2.99 2.38 0.82 1.571 7083 6413 2017 1788 1784 1555 2955 2737 2611 2393 1.46 1.54 1.52 1.8 1.17 0.549

Total number of rows: 28560

Table truncated, full table size 7497 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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