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Sequencing of LPS-stimulated immune cells from chicken

ABSTRACT: Sequencing of LPS-stimulated immune cells from chicken

PROVIDER: PRJEB7475 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR652848_1.fastq.gz	Fastqsanger.gz
	ERR652848_2.fastq.gz	Fastqsanger.gz
	ERR652849_1.fastq.gz	Fastqsanger.gz
	ERR652849_2.fastq.gz	Fastqsanger.gz
	ERR652850_1.fastq.gz	Fastqsanger.gz

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Sequencing of LPS-stimulated immune cells from chicken

Project description:RNAs were analysed from bone marrow derived dendritic cells from 6 week old birds (control and LPS stimulated), bone marrow derived macrophages from 6 week old birds (control and LPS stimulated) and heterophils isolated from blood of day-old chicks (control and LPS stimulated).

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m6A sequencing analysis of chicken hepatic mRNA under normal and LPS stimulated conditions

Project description:Here, the m6A modification patterns in chicken liver at the acute stage of LPS-stimulated inflammation and at the normal state were explored via m6A and RNA sequencing and bioinformatics analysis. A total of 7815 m6A peaks distributed in 5066 genes were identified in the normal chicken liver, and were mostly located in the CDS, 3’UTR region and around the stop codon. At 2 h after the LPS intraperitoneal injection, the m6A modification pattern changed, and showed 1200 different m6A peaks. The hyper- and hypo-m6A peaks were differentially located, with the former mostly located in the CDS region and the later in the 3’UTR and in the region near the stop codon. The hyper- or hypo methylated genes were enriched in different GO ontrology and pathways. Co-analysis revealed a significantly positive relationship between the fold change of m6A methylation level and the relative fold change of mRNA expression. Moreover, protein and protein interaction analysis showed that genes with altered m6A methylation and mRNA expression levels were clustered in processes involved in lipid metabolism, immune response, DNA replication and protein ubiquitination. CD18 and SREBP-1 were the two hub genes clustered in the immune process and lipid metabolism, respectively. Hub gene AGPAT2 was suggested to link the immune response and lipid metabolism clusters in the PPI network. This study presented the first m6A map of broiler chicken liver at the acute stage of LPS induced inflammation. The findings may shed lights on the possible mechanisms of m6A-mediated lipid metabolism disorder in inflammation.

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Chicken erythrocytes stimulated with LPS, PGN and Poly(I:C)

Project description:Erythrocytes represent the most abundant cell type of the bloodstream in all vertebrates. The principal feature that differenciates erythrocytes of non-mammals is that unlike mammals they mantain the nucleus in their terminal differentiation. While the main function associated to erythrocytes is the oxygen and carbon dioxide transport, some other functions, no less important, have been attributed to these cells. The focus of this study was to investigate the response of cultured chicken erythrocytes to bacterial lipopolysaccharide (LPS), bacterial peptidoglycan (PGN) and to the analog viral dsRNA Poly(I:C) using a comercial microarray platform from Agilent. Chicken erythrocytes were isolated from blood by twice Ficoll 1.007 density gradient centrifugations. For primary cell culture, erythrocytes were resuspended in DMEM (PAA Laboratories) supplemented with 10% heat-inactivated fetal bovine serum (FBS, PAA Laboratories) and the antibiotic Primocin (100 μg/ml, Invivogen) at a density of 7.5x106 cells/ml in six well cell culture plates (NUNC) and cultured at 37ºC and 5% CO2. Erythrocytes were stimulated with LPS from E. coli (serotype 0111:B4, Sigma) and Poly(I:C) (Invivogen) at 50 μg/ml, and with peptidoglycan from E.coli (0111:B4, Invivogen) at 5 μg/ml. All culture plates were incubated for 12h. Total RNA was extracted from the cultures using 1 ml of Tri Reagent (Sigma) following the manufacturer’s instructions with minor modifications. Quantity and integrity was analyzed by Nanodrop1000 (ThermoScientific) and Bioanalyzer 2100 (Agilent Technologies) respectively. Three biological replicates were used.

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Immune-stimulated Peyer's patch

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