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Sample GSM566749 Query DataSets for GSM566749
Status Public on Jul 21, 2011
Title Gene expression profiling of type 2b single fiber of mouse skeletal muscle (EDL5)
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 2B single myofibre isolated by enzymatic digestion (test)
Organism Mus musculus
Characteristics tissue: EDL whole muscle
myofiber type: type 2B
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 2B 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 0.91412194 845 7039 120 283 231 2 3 4162 4015 936.17 98 118 81.85 100 100 0 4064 3917 50.85 19407 18426 3847.1 590 606 117.1 100 100 0 18817 17836 165.73 4.63 4.55 4.61 4.64 0.68 3.79 0.85 2.211 22881 21753 4162 4015 4064 3917 8368 7945 8114 7691 2 1.96 1.99 2 1.63 0.997
2 0.919291994 1000 7038 114 252 254 6 3 4443 4387 673.45 98 118 77.92 100 100 0 4345 4289 57.02 20809 20169 2806.71 598 599 125.78 100 100 0 20211 19571 165.45 4.65 4.56 4.59 4.58 0.37 3.73 0.8 2.218 24556 23860 4443 4387 4345 4289 8973 8697 8715 8439 2.01 1.97 1.98 1.98 1.61 1.004
3 0.839040401 1164 7038 114 252 231 2 3 4063 3890 868.91 109 119 40.15 100 100 0 3954 3781 101.19 17950 17554 3675.7 588 590 123.5 100 100 0 17362 16966 145.35 4.39 4.49 4.51 4.59 0.87 3.69 0.76 2.135 21316 20747 4063 3890 3954 3781 7740 7569 7486 7315 1.89 1.93 1.94 1.98 1.59 0.921
4 0.860625847 1326 7038 114 251 231 2 3 4374 4101 1015.14 124 129 39.86 100 99.2 0 4250 3977 109.72 19580 18691 4315.96 610 626 122.51 100 100 0 18970 18081 159.82 4.46 4.55 4.51 4.72 1.48 4 0.88 2.158 23220 22058 4374 4101 4250 3977 8443 8059 8180 7796 1.92 1.96 1.94 2.04 1.72 0.945
5 3.082125433 3897 7034 132 344 116 7 3 136 146 49.96 130 129 41.44 24.7 11 0 6 16 3.28 709 721 151.9 641 645 101.63 37.8 20.9 0 68 80 6.98 11.33 5 4.27 6.67 7.02 2.52 0.69 3.503 74 96 136 146 6 16 306 311 29 34 4.89 2.16 1.84 2.87 1.09 2.289
6 -1.671772994 4057 7035 85 134 311 8 1 125 126 36.49 120 168 244.45 0 0 0 5 6 0.51 663 686 138.67 668 871 1151.17 0 0 0 -4 18 0.58 -1 3 2.72 6.81 10.5 2.72 0.51 0 0 24 125 126 5 6 288 298 -1 8 -0.43 1.3 1.18 2.96 1.18 -1.203
7 -2.292364491 4212 7027 85 137 311 1 1 133 134 37.69 125 132 44.14 16.1 0.7 0 8 9 3.01 644 637 96.72 674 698 178.35 2.9 0 0 -29 -36 3.61 -3.75 -4.11 1.39 2.09 1.83 1.82 0.5 0 -22 -28 133 134 8 9 280 277 -12 -15 -1.63 -1.79 0.6 0.91 0.79 -1.203
8 0.146589382 4374 7048 85 138 311 20 1 131 127 38.09 131 155 92.98 0 0 0 0 -3 1.41 687 730 177.87 713 768 267.32 10.9 0 0 -25 17 2.57 1 -4.25 5.03 5.84 3.68 3.97 0.72 0 -26 13 131 127 0 -3 299 317 -10 7 0.43 -1.85 2.19 2.54 1.73 -1.203
9 -2.844804454 4546 7024 85 137 311 14 1 141 148 44.76 129 133 38.84 20.4 7.3 0 12 19 3.63 643 641 108.95 647 675 153.56 5.1 0.7 0 -3 -5 4.19 -0.33 -0.32 1.72 2.08 1.64 2.03 0.69 0 8 13 141 148 12 19 279 279 -1 -2 -0.14 -0.14 0.75 0.9 0.88 -1.203
10 0.146589382 4692 7031 85 139 311 3 1 119 123 31.64 140 142 39.77 2.9 0 0 -20 -16 2.99 615 625 118.81 684 713 161.1 3.6 0 0 -68 -58 3.82 3.29 3.47 4.4 6.99 8.12 3.03 0.65 1.716 -90 -76 119 123 -20 -16 267 272 -29 -25 1.43 1.51 1.91 3.04 1.32 0.514
11 -3.273005801 4865 7033 85 138 311 13 1 139 145 47.42 123 130 37.1 31.2 11.6 0 16 22 3.75 632 655 161.21 707 711 135.29 10.1 4.3 0 -74 -51 4.67 -4.69 -2.36 1.38 2.66 3.13 2.25 0.44 0 -59 -30 139 145 16 22 275 285 -32 -22 -2.04 -1.03 0.6 1.15 0.98 -1.203
12 0.8921264 848 7195 126 316 116 2 3 4363 4106 963.97 105 107 35.98 100 100 0 4258 4001 121.27 20000 19067 4266.84 571 575 111.28 100 100 0 19429 18496 179.72 4.56 4.62 4.6 4.73 1.07 3.79 0.73 2.19 23687 22497 4363 4106 4258 4001 8624 8221 8377 7975 1.97 1.99 1.98 2.04 1.63 0.976
13 -0.515528269 1010 7160 85 137 311 33 1 306 312 122.85 98 339 852.32 0 0 0 208 214 0.36 901 928 209.64 568 1699 4049.08 0 0 0 333 360 0.22 1.6 1.68 1.69 1.78 0.72 1.45 0.72 0.679 541 574 306 312 208 214 392 403 145 156 0.7 0.73 0.73 0.77 0.63 -0.524
14 0.239403217 1167 7170 90 153 311 22 3 3443 3317 851.63 101 176 402.64 100 99.3 0 3342 3216 8.55 10164 9479 2278.77 578 896 1762.73 100 97.4 0 9586 8901 5.77 2.87 2.77 2.79 2.81 0.44 2.4 0.8 1.52 12928 12117 3443 3317 3342 3216 4383 4087 4133 3838 1.24 1.19 1.2 1.21 1.04 0.307
15 1.123229113 1330 7166 85 135 311 26 1 239 244 60.74 119 164 263.19 0 0 0 120 125 0.91 1204 1166 273.23 606 876 1578.98 0 0 0 598 560 0.76 4.98 4.48 4.61 9.38 38.29 3.71 0.68 2.317 718 685 239 244 120 125 523 507 260 243 2.17 1.95 2 4.07 1.61 1.115
16 1.281137395 1490 7166 102 201 231 25 3 1399 1362 289.8 105 106 31.02 100 100 0 1294 1257 45.1 8012 7906 1077.87 542 565 93.47 100 100 0 7470 7364 85.72 5.77 5.86 5.86 6.1 1.2 3.01 0.66 2.529 8764 8621 1399 1362 1294 1257 3455 3409 3221 3175 2.49 2.53 2.53 2.63 1.3 1.316
17 0.146589382 1636 7197 85 136 311 12 1 87 92 26.7 96 109 49.41 3.7 0 0 -8 -3 1.76 525 546 79.53 567 597 138.39 3.7 0 0 -41 -20 3.79 4.67 5.25 3.53 4.84 4.82 2.41 0.65 2.222 -51 -25 87 92 -8 -3 228 237 -17 -8 2.03 2.28 1.53 2.1 1.05 1.02
18 0.006504301 1810 7164 116 266 254 27 3 1746 1544 616.27 116 119 38.18 98.5 97 0 1630 1428 45.73 4552 4017 1499.08 639 656 136 95.1 93.2 0 3913 3378 33.47 2.4 2.37 2.34 2.46 1.19 2.31 0.9 1.263 5543 4806 1746 1544 1630 1428 1963 1732 1687 1457 1.04 1.02 1.01 1.06 1 0.05
19 0.206223263 1967 7163 96 179 311 27 3 25045 23553 5136.98 116 121 37.28 100 100 0 24929 23437 671.82 65535 63724 6984.9 645 671 143.92 100 100 50.3 64890 63079 455.36 2.6 2.69 2.6 2.87 0.93 1.06 0.61 1.38 89819 86516 25045 23553 24929 23437 28258 27477 27980 27199 1.12 1.16 1.12 1.24 0.46 0.167
20 0.715368867 2126 7164 108 226 208 26 3 915 844 250.38 93 98 29.27 100 100 0 822 751 31.26 3839 3670 896.48 580 601 107.23 99.6 98.7 0 3259 3090 35.8 3.96 4.11 4.05 4.22 0.82 3.27 0.84 1.987 4081 3841 915 844 822 751 1655 1582 1405 1332 1.71 1.77 1.74 1.82 1.41 0.774

Total number of rows: 28560

Table truncated, full table size 7470 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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