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Transcriptome analysis of ΔLMP1-MAVS transfected MARC-145 cells

ABSTRACT: Transcriptome analysis of ΔLMP1-MAVS transfected MARC-145 cells

PROVIDER: PRJNA437302 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6814930_1.fastq.gz	Fastqsanger.gz
	SRR6814930_2.fastq.gz	Fastqsanger.gz
	SRR6814931_1.fastq.gz	Fastqsanger.gz
	SRR6814931_2.fastq.gz	Fastqsanger.gz
	SRR6814932_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of ΔLMP1-MAVS transfected MARC-145 cells

Project description:We found that fuse ΔLMP1 to MAVS could strengthen MAVS mediated inhibition of PRRSV replication in MARC-145 cells. To better understand the biological function of the fusion protein ΔLMP1-MAVS, overall gene expression of MARC-145 cells transfected with ΔLMP1-MAVS or MAVS was evaluated by mRNA-seq. The result showed that ΔLMP1-MAVS upregulated a number of genes associated with innate immune responses to viral infection, including plenty of interferon-stimulated genes. This study provides reference date to research the working mechanism of ΔLMP1-MAVS.

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Differential gene expression between WT MARC-145 cells and MARC-145 cells stably expressing Non-Structural Protein 11 of Porcine Respiratory and Reproductive Syndrome Virus

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Differential gene expression between WT MARC-145 cells and MARC-145 cells stably expressing Non-Structural Protein 11 of Porcine Respiratory and Reproductive Syndrome Virus

Project description:Porcine respiratory and reproductive syndrome virus (PRRSV) is a virus infecting swine and causes swine abortion. Previously, non-structural protein 11 (Nsp11) from PRRSV was shown to have inhibitory function to type I IFN signaling. In this project, we want to see in addition to type I IFN, whether other cellular pathways are influenced by Nsp11 systemtically. A cell line stably expressing PRRSV Nsp11 was established, designated as MARC-Nsp11 cells, and an RNA microarray was conducted using these cells and WT MARC-145 cells MARC-145 and MARC-Nsp11 cells were seeded one day prior to experiments and total cellular RNAs were extracted using Trizol (Invitrogen) and purified by RNeasy mini kit (Qiagen). The quantity and quality of RNA were determined using an Align 2100 bioanalyzer (Agilent Technologies, Palo, Alto, CA, USA), and the RNA integrity was determined above 7. The RNA samples were then subjected to microarray using Human Gene 1.0 ST arrays (Affymetrix UK Ltd, High Wycombe, UK) at the Keck Biotechnology Center, University of Illinois, Urbana, IL). The microarray was repeated twice in duplicates each.

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Effect of SRCAP on gene expression during PRRSV infection of Marc-145 cells.

Project description:To investigate the SRCAP regulation of gene transcription during PRRSV infection, we established Marc-145 cell lines in which SRCAP gene has been knocked down by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq.

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Project description:Effect of SRCAP on gene expression during PRRSV infection of Marc-145 cells.

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Project description:MARC-145 cells were infected with porcine reproductive and respiratory syndrome virus (PRRSV)-2 isolate SD95-21 (KC469618.1), and a mutant thereof (KO2), and subjected to ribosome profiling to analyse the viral and host translatome, frameshifting on the viral genome, and putative frameshift-related ribosome pausing events. Samples were harvested at 9 hpi by flash-freezing, without cycloheximide pre-treatment. RNase I treatment was carried out, following which ribosomes and enclosed RNA were isolated by centrifugation through a sucrose cushion. RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 19-80nt long. Fragments were cloned into adapters based on the TruSeq small RNA adapters, with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a paired-end run. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate.

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