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Sample GSM566764 Query DataSets for GSM566764
Status Public on Jul 21, 2011
Title Gene expression profiling of type 1 single fiber of mouse skeletal muscle (Soleus 2)
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 0.445928214 951 6763 54 50 352 10 3 2348 2176 577.18 145 146 37.15 100 100 0 2203 2031 63.21 5894 5697 1208.41 760 774 94.48 100 100 0 5134 4937 62.38 2.33 2.43 2.47 2.51 0.55 1.77 0.72 1.221 7337 6968 2348 2176 2203 2031 3484 3368 3035 2918 1.38 1.44 1.46 1.49 1.05 0.462
2 0.654853084 1105 6762 54 50 375 4 3 2412 2240 618.61 160 162 44.5 100 100 0 2252 2080 54.2 6846 6356 1531.77 780 791 90.57 100 100 0 6066 5576 75.59 2.69 2.68 2.68 2.8 0.88 2.28 0.85 1.43 8318 7656 2412 2240 2252 2080 4047 3757 3586 3296 1.59 1.58 1.58 1.65 1.35 0.671
3 0.502164062 1261 6764 54 50 375 4 3 2577 2375 676.99 152 157 42.67 100 100 0 2425 2223 60.39 6686 6379 1564.89 810 816 78.63 100 100 0 5876 5569 85.04 2.42 2.51 2.55 2.62 0.63 2 0.75 1.277 8301 7792 2577 2375 2425 2223 3952 3771 3473 3292 1.43 1.48 1.51 1.55 1.18 0.518
4 0.620088027 1423 6763 54 51 375 4 3 2751 2613 778.08 152 157 42.35 100 100 0 2599 2461 64.96 7638 7208 1643.39 804 807 83.44 100 100 0 6834 6404 91.54 2.63 2.6 2.56 2.75 0.75 1.93 0.84 1.395 9433 8865 2751 2613 2599 2461 4515 4261 4040 3785 1.55 1.54 1.51 1.62 1.14 0.636
5 0.118399209 3976 6765 48 37 443 8 3 176 207 72.74 134 141 36.06 73 32.4 0 42 73 4.88 870 894 143.03 792 797 82.81 48.6 32.4 0 78 102 10.51 1.86 1.4 1.6 1.97 0.89 1.48 0.57 0.893 120 175 176 207 42 73 514 528 46 60 1.1 0.83 0.94 1.16 0.88 0.135
6 -4.681576182 4134 6761 85 137 334 8 1 152 156 34.12 137 137 35.25 30.7 3.6 0 15 19 4.31 789 805 95.46 789 793 100.85 18.2 5.1 0 0 16 7.82 0 0.84 1.3 2.14 1.95 1.76 0.4 0 15 35 152 156 15 19 466 476 0 9 0 0.5 0.77 1.26 1.04 -0.759
7 1.264842777 4296 6764 85 135 311 9 1 147 152 35.58 138 139 31.57 31.1 7.4 0 9 14 4.66 828 824 96.82 791 790 84.14 31.1 9.6 0 37 33 9.84 4.11 2.36 2.81 3.17 1.83 2.23 0.67 2.04 46 47 147 152 9 14 489 487 22 19 2.43 1.39 1.66 1.87 1.32 1.28
8 2.395239415 4457 6757 85 135 311 2 1 143 149 39.64 143 142 37.07 19.3 9.6 0 0 6 3.86 814 819 74.41 805 806 85.61 22.2 1.5 0 9 14 9.51 1 2.33 2.53 3.63 4.79 1.4 0.56 0 9 20 143 149 0 6 481 484 5 8 0.59 1.38 1.5 2.14 0.83 -0.759
9 4.269708533 4616 6764 85 136 288 9 1 141 145 34.7 141 143 35.98 11 5.1 0 0 4 3.92 827 823 89.56 794 800 92.93 22.1 4.4 0 33 29 8.9 1 7.25 4.45 6.41 5.08 1.6 0.38 0 33 33 141 145 0 4 489 486 19 17 0.59 4.28 2.63 3.79 0.94 -0.759
10 2.779903265 4773 6761 54 50 352 8 3 151 158 35.43 139 139 34.02 16 8 0 12 19 4.44 914 907 102.68 773 779 89.52 72 30 0 141 134 10.21 11.75 7.05 9.11 10.88 7.35 2.03 0.49 3.555 153 153 151 158 12 19 540 536 83 79 6.95 4.17 5.38 6.43 1.2 2.796
11 0.225314413 4941 6767 85 134 311 12 1 150 148 37.95 144 149 39.96 14.2 3 0 6 4 3.75 802 829 111.73 790 807 92.63 31.3 14.9 0 12 39 8.66 2 9.75 3.81 5.99 6.48 2.16 0.54 1 18 43 150 148 6 4 474 490 7 23 1.18 5.76 2.25 3.54 1.28 0.241
12 0.656236115 948 6917 48 40 443 6 3 2984 2812 528.98 150 156 41.74 100 100 0 2834 2662 71.5 8429 7873 1276.3 788 792 94.44 100 100 0 7641 7085 89.25 2.7 2.66 2.69 2.76 0.75 1.53 0.4 1.431 10475 9747 2984 2812 2834 2662 4982 4654 4517 4188 1.59 1.57 1.59 1.63 0.9 0.672
13 -0.422774626 1114 6916 60 64 375 12 3 1759 1676 610.1 159 159 35.65 100 100 0 1600 1517 49.33 2839 2729 638.42 797 810 113.4 100 100 0 2042 1932 25.04 1.28 1.27 1.27 1.37 0.39 0.94 0.81 0.352 3642 3449 1759 1676 1600 1517 1678 1613 1207 1142 0.75 0.75 0.75 0.81 0.56 -0.407
14 -0.03075672 1272 6918 60 66 375 11 3 3596 3932 1690.86 165 163 34.51 100 100 0 3431 3767 104.2 6534 6517 1959.54 788 814 107.97 100 100 0 5746 5729 60.52 1.67 1.52 1.55 1.78 1.02 0.98 0.71 0.744 9177 9496 3596 3932 3431 3767 3862 3852 3396 3386 0.99 0.9 0.91 1.05 0.58 -0.015
15 0.76489701 1444 6922 66 79 352 23 3 532 547 144.83 166 165 38.89 96.2 94.9 0 366 381 13.68 1845 1868 321.65 781 791 80.82 100 98.7 0 1064 1087 22.83 2.91 2.85 2.87 12.25 59.73 1.69 0.58 1.54 1430 1468 532 547 366 381 1091 1104 629 643 1.72 1.69 1.69 7.24 1 0.781
16 0.97873725 1599 6917 66 78 375 17 3 1331 1192 339.63 163 160 42.96 100 100 0 1168 1029 30.98 4742 4551 1244.56 804 806 88.58 100 100 0 3938 3747 53.54 3.37 3.64 3.75 4.01 1.91 2.88 0.62 1.753 5106 4776 1331 1192 1168 1029 2803 2690 2328 2215 1.99 2.15 2.22 2.37 1.7 0.995
17 2.032669335 1743 6919 85 136 288 3 1 143 150 41.7 168 168 45.86 7.4 0.7 0 -24 -17 3.12 837 842 103.55 830 821 79.63 25 8.1 0 7 12 10.51 -0.28 -0.67 3.49 8.58 17.21 1.92 0.6 0 -18 -6 143 150 -24 -17 495 497 4 7 -0.17 -0.39 2.06 5.07 1.14 -0.759
18 0.530479712 1912 6918 60 65 398 11 3 1594 1522 528.03 157 160 42.24 100 98.5 0 1437 1365 37.73 4363 4192 1173.37 812 814 91.71 100 100 0 3551 3380 47.58 2.47 2.48 2.54 2.78 1.48 1.86 0.7 1.305 4988 4745 1594 1522 1437 1365 2579 2478 2099 1998 1.46 1.46 1.5 1.64 1.1 0.547
19 0.190119878 2076 6924 66 76 375 18 3 33298 30757 11273.25 165 167 38.62 100 100 0 33133 30592 862.25 65535 61988 10588.55 866 868 97.83 100 100 50 64669 61122 669.86 1.95 2 1.95 2.56 1.91 0.58 0.38 0.965 97802 91714 33298 30757 33133 30592 38738 36641 38226 36129 1.15 1.18 1.15 1.51 0.34 0.206
20 1.133285275 2244 6924 66 77 398 25 3 947 975 307.56 146 152 37.73 100 100 0 801 829 25.1 3806 3576 791.68 800 815 101.79 100 100 0 3006 2776 37.39 3.75 3.35 3.4 3.67 1.48 2.3 0.8 1.908 3807 3605 947 975 801 829 2250 2114 1777 1641 2.22 1.98 2.01 2.17 1.36 1.149

Total number of rows: 28560

Table truncated, full table size 7464 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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