Unknown,Transcriptomics,Genomics,Proteomics

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Single-cell and single-nucleus RNAseq of the human and mouse skeletal muscle across age

ABSTRACT: This study aims to characterize the diversity of cell types in human skeletal muscle across age using two complementary technologies: single-cell and single-nucleus sequencing, which provide a comprehensive coverage of cell types in the muscle. We leveraged the aforementioned datasets to study change in cell type composition and gene expression between young (n= 8, approx. 20-40 yrs) and old (n = 9, approx. 60-80 yrs) adults, highlighting changes in the major skeletal muscle compartments, muscle satellite cells, myofiber and muscle microenvironment including stromal, immune and vascular cell types. Additionally, we generated a complementary mouse muscle aging dataset by profiling hindlimb muscles from young (n = 5, 3 months) versus old mice (n = 3, 19 months), using single-cell and single-nucleus sequencing for comparison.

INSTRUMENT(S): Illumina NovaSeq 6000, Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Veronika Kedlian

PROVIDER: E-MTAB-13874 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:TLR4/NF-ÎºB signaling plays a central mediator in response to danger signals released in the muscle ischemia-reperfusion injury (IRI). This study was designed to profile TLR4/NF-ÎºB-responsive microRNAs (miRNAs) in the skeletal muscles following IRI. Following 2 h of ischemia and subsequent reperfusion for indicated times (0 h, 4 h, 1 d, and 7 d) of the isolated thigh skeletal muscles based on femoral artery perfusion of C57BL/6, Tlr4â/â, and NF-ÎºBâ/âmice, the muscle specimens were analyzed with an miRNA array to detect the TLR4/NF-ÎºB-responsive miRNAs. Male C57BL/6 mice (10â12 weeks of age, 22â35 g) were purchased from BioLasco (Taiwan). Tlr4â/â (C57BL/10ScNJ) and NF-ÎºBâ/â (B6.Cg-Nfkb1tm1Bal/J) mice were purchased from Jackson Laboratory (Bar Harbor, ME, USA). All housing conditions were established and surgical procedures, analgesia, and assessments were performed in an AAALAC-accredited, SPF facility following national and institutional guidelines. Animal protocols were approved by the IACUC of Chang Gung Memorial Hospital. Mice were anesthetized with an anesthetic cocktail consisting of 0.1 mg/g ketamine and 0.01 mg/g xylazine, given as an intraperitoneal injection (0.01 ml/g body weight). After the induction of anesthesia, the mice were restrained in a supine position on a heating pad to maintain body temperature at 37Â°C. The quadriceps muscle perfused based on the femoral artery of the mouse was carefully isolated away from the femoral bone and the underlying adductor muscle group. In the ischemic group, ischemia was induced by placing a microvascular clamp carefully across the proximal site of vascular pedicle for 2 h and then the microvascular clamp was removed. Good vascular inflow and outflow through the pedicle was verified under direct magnified vision. In the sham-operated control group, the muscle was isolated without microvascular clamp being applied. The incision wound was closed with interrupted sutures (4-0 nylon) and the animals were allowed to awaken in the remaining periods of reperfusion. The harvested muscles were frozen in isopentane chilled in liquid nitrogen and stored at -80Â°C. For the miRNA array experiments, the isolated skeletal muscles of C57BL/6 mice after 2 h of ischemia and 0 h, 4 h, 1 d, and 7 d of reperfusion as well as of Tlr4â/âand NF-ÎºBâ/â mice after 2 h of ischemia and 1 d of reperfusion were used in 3 replicate experiments.

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Single-cell and single-nucleus RNAseq of the human and mouse skeletal muscle across age

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