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Sample GSM566750 Query DataSets for GSM566750
Status Public on Jul 21, 2011
Title Gene expression profiling of type 2b single fiber of mouse skeletal muscle (EDL6)
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 0.582781705 983 7320 114 252 231 10 3 12586 12003 2030.84 180 183 78.68 100 100 0 12406 11823 159.97 23942 22689 4977.23 678 712 178.11 100 100 0 23264 22011 134.42 1.88 1.86 1.88 1.86 0.27 2.09 0.73 0.907 35670 33834 12586 12003 12406 11823 20952 19855 20358 19262 1.64 1.63 1.64 1.63 1.83 0.715
2 0.496596051 1140 7322 108 227 231 12 3 12028 11844 2178.31 192 191 72.33 100 100 0 11836 11652 166.3 21513 21087 4494.7 729 754 196.23 100 100 0 20784 20358 109.63 1.76 1.75 1.74 1.75 0.24 1.81 0.77 0.812 32620 32010 12028 11844 11836 11652 18826 18453 18188 17815 1.54 1.53 1.52 1.53 1.58 0.62
3 0.55630739 1300 7321 108 227 231 11 3 11672 11555 2546.77 183 189 75.06 100 100 0 11489 11372 155.5 21730 20112 5333.86 718 730 196.3 100 100 0 21012 19394 110.7 1.83 1.71 1.72 1.69 0.2 1.97 0.89 0.871 32501 30766 11672 11555 11489 11372 19016 17600 18388 16972 1.6 1.49 1.51 1.48 1.73 0.678
4 0.496465484 1461 7321 108 227 208 10 3 11192 11024 2594.54 182 185 85.51 99.1 98.2 0 11010 10842 130.89 19884 19168 4739.76 666 665 181.88 100 100 0 19218 18502 109.32 1.75 1.71 1.72 2.11 3.87 1.64 0.81 0.804 30228 29344 11192 11024 11010 10842 17401 16774 16818 16191 1.53 1.49 1.51 1.85 1.44 0.611
5 1.26963882 4015 7310 66 80 375 4 3 267 324 145.1 180 191 85.24 56.3 45 0 87 144 3.13 889 852 137.67 721 730 180.26 42.5 2.5 0 168 131 4.93 1.93 0.91 1.28 1.44 0.93 0.74 0.6 0.949 255 275 267 324 87 144 778 746 147 115 1.69 0.8 1.12 1.26 0.65 0.757
6 6.306830264 4172 7310 85 137 288 7 1 148 156 64.83 172 175 64.34 6.6 4.4 0 -23 -15 2.3 684 693 160.7 675 695 138.01 19 8 0 9 18 4.96 -0.38 -1.13 5.63 11.24 18 2.1 0.72 0 -15 2 148 156 -23 -15 598 605 8 16 -0.33 -0.98 4.92 9.82 1.83 -0.195
7 6.537333687 4330 7305 85 134 311 9 1 151 166 81.32 159 167 60.76 20.9 7.5 0 -7 7 2.49 682 699 176.32 672 686 139.67 27.6 7.5 0 10 27 4.88 -1.25 3.86 2.65 6.09 16.46 1.44 0.44 0 2 34 151 166 -7 7 596 611 9 24 -1.09 3.37 2.31 5.32 1.26 -0.195
8 -1.048687566 4496 7306 85 134 288 4 1 179 162 63.57 152 162 61.79 24.6 3 0 27 10 2.9 636 650 95 692 696 155.84 2.2 0 0 -55 -41 4.08 -2.07 -4.2 0.99 1.4 1.27 1.12 0.56 0 -29 -32 179 162 27 10 556 568 -48 -36 -1.81 -3.67 0.87 1.22 0.98 -0.195
9 0.060293941 4653 7311 85 136 288 4 1 151 151 61 155 166 71.7 8.8 1.5 0 -3 -3 2.11 553 585 131.8 628 633 129.16 8.1 3.7 0 -74 -42 4.28 18.75 10.75 2.16 3.73 4.72 1.62 0.56 4.229 -79 -47 151 151 -3 -3 483 511 -65 -37 16.38 9.39 1.89 3.26 1.42 4.034
10 0.060293941 4820 7309 85 136 288 3 1 155 171 80.99 156 163 65.6 23.5 11 0 0 15 2.36 522 566 142.96 657 666 165.35 8.1 1.5 0 -134 -90 3.16 135 -6.07 1.76 2.14 1.91 1.17 0.44 7.077 -136 -76 155 171 0 15 456 494 -117 -78 117.93 -5.3 1.54 1.87 1.02 6.882
11 1.020997796 4973 7313 150 447 84 4 3 189 203 79.14 131 153 82.98 43.2 12.8 0 58 72 2.28 708 733 200.5 611 630 141.63 38.3 17.4 0 97 122 5 1.67 1.69 1.85 2.56 2.8 1.5 0.35 0.742 155 194 189 203 58 72 620 641 85 107 1.46 1.48 1.62 2.24 1.31 0.549
12 0.568597586 985 7476 126 312 139 8 3 13532 12460 3777.42 184 186 71.22 99.4 98.7 0 13348 12276 189.99 25602 23294 7133.76 692 701 148.98 100 99.7 0 24910 22602 171.85 1.87 1.84 1.86 2.73 13.92 1.78 0.89 0.9 38258 34878 13532 12460 13348 12276 22404 20385 21799 19779 1.63 1.61 1.63 2.39 1.56 0.708
13 -0.508289466 1137 7450 78 115 288 19 3 3547 3496 836.34 192 567 1585.21 97.4 60.9 0 3355 3304 2.24 3162 3246 781.37 774 1308 2652.64 36.5 0 0 2388 2472 1.19 0.71 0.75 0.72 0.75 0.14 0.76 0.66 -0.491 5743 5776 3547 3496 3355 3304 2767 2841 2090 2163 0.62 0.65 0.63 0.66 0.66 -0.683
14 0.385812124 1301 7449 108 227 231 19 3 13247 12578 4563.6 176 450 1469.53 96 93.8 0 13071 12402 9.01 22091 21681 8120.58 734 1067 1983.27 99.6 93.8 0 21357 20947 11.14 1.63 1.69 1.66 1.78 0.64 1.61 0.82 0.708 34428 33349 13247 12578 13071 12402 19332 18973 18690 18331 1.43 1.48 1.45 1.56 1.41 0.516
15 0.724392223 1467 7446 114 256 208 21 3 1480 1461 634 182 454 1329.12 49.2 0 0 1298 1279 1.11 2707 2572 852.28 674 995 1702.48 59.8 1.2 0 2033 1898 1.59 1.57 1.48 1.52 1.73 1.46 1.24 0.85 0.647 3331 3177 1480 1461 1298 1279 2369 2251 1779 1661 1.37 1.3 1.33 1.51 1.08 0.455
16 1.453232303 1616 7449 108 222 208 20 3 7175 6714 1905.6 139 154 69.89 100 100 0 7036 6575 102.67 24265 22385 5794.93 667 687 160.9 100 99.5 0 23598 21718 150.81 3.35 3.3 3.37 3.38 0.79 2.75 0.82 1.746 30634 28293 7175 6714 7036 6575 21234 19589 20651 19006 2.94 2.89 2.95 2.96 2.41 1.553
17 8.262067461 1789 7461 85 135 311 8 1 140 166 61.43 150 156 60.26 28.9 3 0 -9 16 2.32 714 734 193.24 690 718 173.61 23.7 8.1 0 24 44 4.11 -2.4 2.75 2.44 4.17 4.71 2.38 0.57 0 14 60 140 166 -9 16 624 641 21 38 -2.1 2.4 2.13 3.64 2.08 -0.195
18 -1.096941594 1936 7445 102 201 208 24 3 11244 10655 2917.34 170 171 61.71 99 99 0 11074 10485 182.21 6799 6288 1593.98 734 755 178.13 100 98.5 0 6065 5554 38.17 0.55 0.53 0.53 0.61 0.67 0.51 0.89 -0.869 17139 16039 11244 10655 11074 10485 5950 5503 5308 4860 0.48 0.46 0.46 0.54 0.45 -1.061
19 -0.414719409 2093 7445 102 200 254 24 3 65535 59086 16763.01 142 179 82.49 100 100 50 65393 58944 794.45 65535 62199 11959.82 636 670 167.73 100 100 50 64899 61563 390.71 0.99 1.04 0.99 1.43 1.78 0.56 0.61 -0.011 130292 120507 65535 59086 65393 58944 57350 54431 56794 53874 0.87 0.91 0.87 1.25 0.49 -0.203
20 1.162695834 2254 7448 96 175 311 21 3 2228 2309 710.19 171 180 71.5 99.4 98.9 0 2057 2138 31.16 5379 5379 1242.01 659 684 153.53 100 100 0 4720 4720 35.04 2.29 2.21 2.28 2.36 0.82 1.24 0.5 1.198 6777 6858 2228 2309 2057 2138 4707 4707 4131 4131 2.01 1.93 2 2.06 1.08 1.006

Total number of rows: 28560

Table truncated, full table size 7396 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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