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ABSTRACT: cgSHAPE_SARS-CoV2-5'UTR mutation detection

PROVIDER: PRJNA950557 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24091630_1.fastq.gz	Fastqsanger.gz
	SRR24091630_2.fastq.gz	Fastqsanger.gz
	SRR24091631_1.fastq.gz	Fastqsanger.gz
	SRR24091631_2.fastq.gz	Fastqsanger.gz
	SRR24091632_1.fastq.gz	Fastqsanger.gz

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Project description:The goal of this study was to determine changes in the expression of genes in monoctic myleoid derived suppressor cells (M-MDSC) as a result of SARS CoV2 infection. The study aimed to investigate if M-MDSC are functionally active and inhibit T cell function in response to SARS CoV2 antigens 5 months after first detection of the virus. Methods: Peripheral blood mononuclear cells (PBMC) were collected from CoV2 (-) and CoV2 (+) donors (N=5 each group). M-MDSC were isolated by flow cytometry, and RNA extracted for RNA-seq studies. Filtering low quality reads and removal of the 3’ adapter sequences were performed using the Trim Galore tool. Reads were mapped to the latest version of the human genome (build hg38) using HISAT2. Mapped reads were counted against the human GENCODE annotation (v37) using HT-Seq. The EdgeR library in the R computing environment was used for quality control of the RNA-Seq data, and ComBat-seq method for correction of batch effects. Differential gene expression analysis was conducted using EdgeR. Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8. Results: An average of 34 million reads per sample were acquired and mapped to the human genome (build hg38). After applying filtering criteria, 9,217 human genes were identified with the HISAT2 and HTSeq workflow. Differential expression analysis was performed between CoV2 (+) and CoV2 (-) samples using EdgeR. A total of 188 differentially expressed genes (DEGs) were identified with nominal p-value <0.05; of which 63 were up- and 125 downregulated in CoV2 (+) samples. A total of 12 DEGs were identified with false discovery rate corrected p-value <0.05, of which 2 were up- and 10 downregulated. Pathway enrichment analysis identified pathways involved in immune response and innate immune signaling. Conclusion: The study demonstrated that CoV2 infection modulated the expression of genes involved in immune response and innate immune signaling. Most of the genes remained downregulated even after 5 months of first detection of SARS CoV2.

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