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Next Generation Sequencing Facilitates Quantitative Analysis of Different Transcriptomes betwwen AA, AG, GG pDCs

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Different Transcriptomes betwwen AA, AG, GG pDCs

PROVIDER: PRJNA735931 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14758135_1.fastq.gz	Fastqsanger.gz
	SRR14758135_2.fastq.gz	Fastqsanger.gz
	SRR14758136_1.fastq.gz	Fastqsanger.gz
	SRR14758136_2.fastq.gz	Fastqsanger.gz
	SRR14758137_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Different Transcriptomes betwwen AA, AG, GG pDCs

Project description:Purpose: NCF1 gene single nucleotide polymorphism (SNP) rs201802880 (G to A change) promotes the activation of plasmacytoid dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation. Methods: Mouse plasmacytoid dendritic cells isolated from GG, AG or AA allele mice, were stimulated with R848 for 12 hours. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/). Results: Genes in the TLR7-IRF7 pathway were augmented by NCF1 SNP. As a result, the production of type I IFNs increased in AA pDCs.

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The rs6967330 minor allele in CDHR3 increased CRS exacerbations and is associated with an exaggerated interferon response to RV-A and RV-C infections

Project description:Background: Adults with at least one copy of the minor allele in the rs6967330 SNP (AA/AG) in the rhinovirus (RV) receptor Cadherin related family member 3 gene (CDHR3), have a higher risk for CRS than those with two copies of the major allele (GG). Objective: To determine if the rs6967330 SNP increased the risk for acute exacerbations of chronic rhinosinusitis (AECRS) in adults and identify if their nasal cells showed a distinct pathophysiologic process activated by RV infection. Methods: We recruited adults with CRS (AG/AA,n=17; GG,n=37) and at baseline collected sinonasal outcome tests (SNOT-22), objective endoscopy scores, and nasal brushings for cells and RV viral detection. Subjects were contacted every two weeks for AECRS over one year, and if symptomatic this data was re-collected. To determine the effect of the rs6967330 SNP, air-liquid-interface (ALI) cultures were derived from nasal samples (AG/AA,n=19; GG,n=19). Cytokines and RNA transcriptome responses were measured 48 hours-post viral challenge with RV-A, RV-B, and RV-C. Results: During AECRS, adults with the AA/AG allele had 1.6x higher SNOT-22 scores, 2x higher endoscopic scores, and were 4x more likely to have RV infections during AECRS than those with the GG allele. (AA/AG) ALI cultures had significantly greater virus replication of RV-A (2.4x) and RV-C (3.5x) but not RV-B, higher levels of inflammatory cytokines, and significantly increased interferon-related pathways compared to (GG) ALI cultures. Conclusions: The minor allele in the rs6967330 SNP increases the risk for AECRS disease severity and is associated with an aberrant interferon-mediated inflammatory response to both RV-A and RV-C infections.

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Differential miRNAs between Sensitive and Resistant Pig to Escherichia coli F18 by deep sequencing

Project description:An M307 G/A point mutation of FUT1 gene has been considered as a usful marker to select the piglets that are sensitive(GG/AG genotype) or resistant(AA) to Escherichia coli F18 in foreign pig breeds. However,it is not suitable to Chinese native breeds. Duodenal tissues were collected from 3 full-sib pairs of Sutai pigs (a new hybrid between the Duroc and Taihu breeds) at the age of 28-day differing in adhesion phenotype to find the differential miRNAs that can provide the basis for analyzing the different mechanisms of E.coli F18 resistance between foreign and Chinese native breeds,as well as for breeding for disease resistance in Chinese native breeds in the future. piglets at the age of 28-day sensitive(GG genotype) to Escherichia coli F18 vs resistant(AA) ones.Biological replicates:3 full-sib pairs of Sutai pigs(3 pairs for GG/AA genotype of FUT1 gene).One GG sample (512 piglet) was sequenced twice to verify the result. 2385 piglet and 2383 piglet were a pair of full-sib with AA and GG genotype at M307 positionof FUT1 gene, respectively. Unfortunately, the sequencing of 2385 was a failure and was excluded. 2385 piglet has an AA genotype of the FUT1 gene

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