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| Status |
Public on Dec 20, 2019 |
| Title |
Expression Signatures of Single Isolated Myofibers of Mouse Hindlimb. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Skeletal muscles are composed by different myofiber types with a wide range of metabolic and functional properties. In the past years, biophysical analyses on isolated muscle fibers were extensively used to study the different contractile features of each myofiber type. To better clarify the complex mechanisms determining and regulating this heterogeneity, we applied genomic technologies at the level of single isolated myofibers. Fibers were prepared from soleus and EDL mouse muscles in order to obtain a comprehensive collection of fiber types classified according to myosin heavy chain (MyHC) isoforms. Transcriptomic analysis performed using microarray technology produced expression profiles of myofibers free from the background of non-contractile cell of the muscles. This permitted to identify a complete catalogue of genes differentially expressed among fiber types, mainly coding for metabolic enzymes, isoforms of the contractile proteins, and proteins involved in calcium homeostasis. Interestingly, myofibers transcriptionally grouped in 3 different transcriptional clusters, named transcriptional slow (tS), intermediate (tI), and fast(tF), mainly according to their metabolism and speed of contraction. This transcriptionally based myofibers grouping only partially fit with myofibers classification based on MyHC isoforms. In addition, using microarray data, we identified a limited set of transcriptional markers that can be used to unequivocally classify myofibers in one of the three clusters (tS, tI, or tF). This approach based on single cell analysis would allow a better description and comprehension of the adaptive transitions at transcriptional level occurring in myofibers under physiological and pathological conditions.
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| Overall design |
EDL and soleus mouse muscles were incubated with type I collagenase (Sigma-Aldrich) to dissociate intact myofibers that were separately collected under stereomicroscope. Isolated myofibers were divided in two parts: one was immersed in Laemmli buffer for fiber typing; the other was placed in TRIzol Reagent (Life Technologies) for RNA purification. Myofibers were classified according to their myosin heavy chain (MyHC) protein isoform in pure MyHC-1, -2A, -2X, -2B, and hybrid Hyb-2A/2X, and -2X/-2B (total: 6 myofiber types). We analyzed the transcription profiles of 10 single isolated myofibers (biological replicas) for each of the 6 patterns of MyHC isoform expression (total: 60 experiments). One-color hybridizations were performed on SurePrint G3 Mouse GE 8x60K Microarrays (Agilent Technologies).
Biological replicates of the same myofiber type were numbered from 1 to 10 and marked with the muscle of origin (S for soleus, and E for EDL) and the number of the animal.
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| Contributor(s) |
Chemello F, Cagnin S, Cancellara P, Martini P, Millino C, Pacchioni B, Romualdi C, Reggiani C, Lanfranchi G |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 28, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Gerolamo Lanfranchi |
| E-mail(s) |
stefano.cagnin@unipd.it
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| Phone |
+39-0498276219
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| Organization name |
University of Padova
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| Department |
CRIBI - Biotechnology Center and Biology Department
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| Lab |
Functional Genomics Lab
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| Street address |
Via U. Bassi, 58/B
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| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
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| Platforms (1) |
| GPL10787 |
Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Probe Name version) |
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| Samples (60)
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| This SubSeries is part of SuperSeries: |
| GSE98328 |
Expression Signatures of Single Isolated Myofibers of Mouse Hindlimb and miR-27a-3p or miR-142-3p overexpression in C2C12 myoblasts |
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| Relations |
| BioProject |
PRJNA384719 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98325_RAW.tar |
723.7 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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