Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Small RNA-seq of quiescent, activated of differentiated mouse skeletal muscle stem cells

ABSTRACT: The requirement for microRNAs in muscle homeostasis, and more precisely in quiescence/self-renewal, activation & differentiation, has been demonstrated through knock-out experiments. In this experiment, we unbiasedly probed the expression of small RNA molecules (ranging from 18-36 nt in size), during the quiescence/activation transition but also differentiation by mean of small-RNA sequencing. Quiescent cells were directly FACS-purified from resting muscle of tg:Pax7-nGFP adult mice (n=2 replicates), and a fraction of these sorted cells were cultured in vitro to obtain activated MuSC at 60h, or differentiated cells at 7 days. This dataset constitutes a key resource for further analyses of miRNAs involvement in the muscle paradigm, and more largely in the regulation of stem cells self-renewal and tissue homeostasis.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Mus musculus

SUBMITTER: David Castel

PROVIDER: E-MTAB-5955 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are type members of Tritimovirus and Poacevirus genera, respectively, in the family Potyviridae, and are transmitted by wheat curl mites. Co-infection of these two viruses causes synergistic interaction with increased virus accumulation and disease severity in wheat. In this study, we examined the effects of synergistic interaction between WSMV and TriMV on endogenous small (s) RNAs and virus-specific small interfering RNAs (vsiRNAs) in susceptible (Arapahoe) and temperature-sensitive resistant (Mace) wheat cultivars at 27C and 18C. Single- and double-infections in wheat caused a shift in the profile of endogenous sRNAs from 24 nt being the most predominant in healthy plants to 21 nt in infected wheat. Additionally, we report high-resolution vsiRNA maps of WSMV and TriMV in singly- and doubly-infected wheat cultivars Arapahoe and Mace at 18C and 27C. Massive amounts of 21 and 22 nt vsiRNA reads were accumulated in Arapahoe at both temperatures and in Mace at 27C but not at 18C. The plus- and minus-sense vsiRNAs were distributed throughout the genomic RNAs in Arapahoe at both temperature regimens and in Mace at 27C, although some regions of genomic RNAs serve as hot-spots with an excessive number of vsiRNAs. The positions of vsiRNA peaks were conserved among wheat cultivars Arapahoe and Mace, suggesting that Dicer-like enzymes of susceptible and resistant wheat cultivars are similarly accessed the genomic RNAs of WSMV and TriMV. Additionally, several cold-spot regions were found in the genomes of TriMV and WSMV with no or a few vsiRNAs, indicating that certain regions of WSMV and TriMV genomes are not accessible to Dicer-like enzymes. The high-resolution map of endogenous and vsiRNAs from wheat cultivars synergistically infected with WSMV and TriMV at two temperature regimens form a foundation for understanding the virus-host interactions, effect of synergistic interactions on host defense mechanisms, and virus resistance mechanisms in wheat. Small RNA was sequenced from two wheat cultivars (Mace and Araphahoe), at two temperatures 18C and 27C, for healthy (control/uninfected), infected with wheat streak mosaic virus (WSMV), infected with Triticum mosaic virus (TriMV), and a double-infecttion of WSMV and TriMV.

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Small RNA-seq of quiescent, activated of differentiated mouse skeletal muscle stem cells

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