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Th1/Th17 cell associated pathways are upregulated in murine cytomegalovirus infected murine kidneys after allogeneic transplantation

ABSTRACT: Th1/Th17 cell associated pathways are upregulated in murine cytomegalovirus infected murine kidneys after allogeneic transplantation

PROVIDER: PRJNA744942 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15076536_1.fastq.gz	Fastqsanger.gz
	SRR15076536_2.fastq.gz	Fastqsanger.gz
	SRR15076537_1.fastq.gz	Fastqsanger.gz
	SRR15076537_2.fastq.gz	Fastqsanger.gz
	SRR15076538_1.fastq.gz	Fastqsanger.gz

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Th1/Th17 cell associated pathways are upregulated in murine cytomegalovirus infected murine kidneys after allogeneic transplantation

Project description:Purpose: To characterize transcriptional profiles of murine cytomegalovirus infected allografts after renal transplantation. Methods: RNA was isolated from murine allografts and native kidneys, with and without MCMV infection. Libraries were generated and paired end 150 base pair sequencing was performed on the HiSeq 4000 (Illumina) (Supplementary Methods). Each sample was aligned to the GRCm38.p4 assembly of the mouse reference from NCBI using version 2.6.0c of the RNA-Seq aligner STAR. Transcript features were identified from the GFF file provided with the assembly from NCBI and raw coverage counts were calculated using HTSeq. The raw RNA-Seq gene expression data was normalized and post-alignment statistical analyses were performed using DESeq2 and custom analysis scripts written in R. Comparisons of gene expression and associated statistical analysis were made between different conditions of interest using the normalized read counts. All fold change values are expressed as test condition/control condition, where values less than 1 are denoted as the negative of its inverse. Results: The QIAGEN Ingenuity Pathway Analysis (IPA) software was used for canonical pathway and differential gene expression analyses. IPA showed that, compared to MCMV infected native kidneys, transplantation of MCMV-infected kidneys led to significant changes in 5502 genes (adjusted p values <0.05), involved in 391 canonical pathways. The Th17 activation pathway showed 107 differentially expressed genes.Th1 pathway was one of the most highly upregulated pathways observed in the MCMV infected allografts. Conclusions: Transcripts for Th1/Th17 cell associated activation and signaling are differentially expressed in MCMV infected kidneys after allogeneic transplantation.

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