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Gene expression profiling of porcine skeletal muscle satellite cells after challenge with poly I:C

ABSTRACT: Porcine satellite cells play a vital role in the construction, development, and self-renewal of skeletal muscle. In this study, porcine satellite cells were exposed to mimic viral infection poly (I:C) during proliferation and differentiation phases at 0h, 12h, 24h and 48h time points. The untreated and treated porcine satellite cells during proliferation and differentiation phases were further analyzed by RNA sequencing technology. In the proliferation and differentiation phases of porcine satellite cells grown under poly (I:C), 88, 119, 104 and 95 genes were differentially expressed in 0h – 12h treated, 12h – 24h treated, 0h – 24h treated and 24h – 48h untreated comparison libraries, respectively. The GO terms analysis results showed that in the proliferation phase of treated porcine satellite cells, the up-regulated genes related to the immune system were highly expressed. In addition, the gene expression associated with muscle structure development, response to growth factor emerged in the differentiation phase of untreated porcine satellite cells. The biological pathways associated with Influenza A, Toll-like signaling as well as chemokine signaling were revealed through poly (I:C) stimulation of porcine satellite cells. The differentially expressed genes were confirmed by quantitative real-time PCR. Our findings expanded the understanding of gene expression and signaling pathways about the infiltrated mechanism of the virus into porcine skeletal muscle satellite cells.

ORGANISM(S): Sus scrofa

PROVIDER: GSE112527 | GEO | 2018/03/31

REPOSITORIES: GEO

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Project description:The aim of the measurements was to investigate RNA damage and RNA-protein crosslinks (RPC) formation in the context of aldehyde-induced toxicity. For this, a photoactivatable-ribonucleoside-enhanced crosslinking (PAR-CL) strategy using 4-thiouridine (4-SU) and UVA-radiation was used. The submitted dataset contains data from LC-MS/MS measurements of crosslinks between proteins and poly-adenylated mRNAs (mRPCs). The measurements included the following six samples sets: Sample set 1 (9 runs = 3 conditions in 3 replicates): RPCs after formaldehyde (FA) and 4-SU + UVA treatment isolated using the protein-x-linked RNA extraction (XRNAX) protocol (doi:10.1016/j.cell.2018.11.004) Conditions: RPCs from untreated HAP1 =Ctrl RPCs from HAP1 treated with FA RPCs from HAP1 treated with 4-SU + UVA Sample set 2 (12 runs = 4 conditions in 3 replicates): mRPCs after 4-SU + UVA treatment using poly-A pulldown Conditions: mRPCs from untreated HAP1=Ctrl mRPCs from HAP1 treated with UVA but without 4-SU (0h after irradiation) mRPCs from HAP1 treated with 4-SU but without UVA mRPCs from HAP1 treated with 4-SU + UVA (0h after irradiation) Sample set 3 (24 runs = 6 conditions in 4 replicates): mRPCs after 4-SU + UVA and Ub-E1i treatment using poly-A pulldown Conditions: mRPCs from HAP1 treated with 4-SU + UVA (0h, 0.5h and 1h after irradiation) mRPCs from HAP1 treated with 4-SU + UVA and Ub-E1i (0h, 0.5h and 1h after irradiation) Sample set 4 (24 runs = 6 conditions in 4 replicates): mRPCs after 4-SU + UVA and MG132 treatment isolated using poly-A pulldown Conditions: mRPCs from HAP1 treated with 4-SU + UVA (0h, 0.5h and 1h after irradiation) mRPCs from HAP1 treated with 4-SU + UVA and MG132 (0h, 0.5h and 1h after irradiation) Sample set 5 (24 runs = 6 conditions in 4 replicates): mRPCs after 4-SU + UVA and ANS treatment using isolated poly-A pulldown Conditions: mRPCs from HAP1 treated with 4-SU + UVA (0h, 0.5h and 1h after irradiation) mRPCs from HAP1 treated with 4-SU + UVA and ANS (0h, 0.5h and 1h after irradiation) Sample set 6 (24 runs = 6 conditions in 4 replicates ): mRPCs after 4-SU+UVA in AAVS1 control and RNF14 KO cells using poly-A pulldown mRPCs from HAP1 AAVS1 control cells (clone #6) treated with 4-SU+UVA (0h, 0.5h and 1h after irradiation) mRPCs from HAP1 RNF15 KO cells (clone #15) treated with 4-SU+UVA (0h, 0.5h and 1h after irradiation) Abbreviations: 4-SU: 4-thiouridine ANS: Anisomycine, a translation elongation inhibitor FA: Formaldehyde MG132: proteasome-inhibitor mRPCs: crosslinks between proteins and poly-adenylated mRNAs isolated by Poly-A pulldown RPCs: crosslinks between proteins and RNA isolated by XRNAX Ub-E1i: ubiquitin E1 inhibitor (E1i, TAK-243) UVA: Ultraviolet A

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Gene expression profiling of porcine skeletal muscle satellite cells after challenge with poly I:C

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