Gene expression analysis of spleens from virus-infected rats
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA470952 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7146530_1.fastq.gz | Fastqsanger.gz | |||
| SRR7146530_2.fastq.gz | Fastqsanger.gz | |||
| SRR7146531_1.fastq.gz | Fastqsanger.gz | |||
| SRR7146531_2.fastq.gz | Fastqsanger.gz | |||
| SRR7146532_1.fastq.gz | Fastqsanger.gz |
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Project description:We infected chickens from two genetic lines, one bred to be resistant to Marek's disease and one bred to be susceptible, with the Marek's disease virus. We performed single-cell RNA sequencing of the spleens of these chickens along with age-matched uninfected controls from both lines.
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Project description:Purpose: Marek's disease virus (MDV) is an oncogenic herpesvirus that can induce T-cell lymphoma. Long noncoding RNA (lncRNA) strongly associated with various cancers and many other diseases. In chickens, lncRNAs have not been comprehensively identified. Here, we profiled mRNA and lncRNA repertoires in three groups of spleens from MDV-infected and non-infected chickens, including seven tumorous spleens (TS) from MDV-infected chickens, five spleens from the survivors (SS) without any lesion after MDV infection, and five noninfected spleens (NS) from chickens, to explore the underlying mechanism of host resistance to Marek's disease (MD). Results: By using precise lncRNA identification pipeline, we identified 1315 putative lncRNAs and 1166 known lncRNAs in spleen tissue. Genomic features of putative lncRNAs were characterized. Differentially expressed mRNAs, putative lncRNAs and known lncRNAs were profiled. Some previously reported MD resistance candidate genes, such as CTLA4, HDAC9 and CD72, were also found in our differentially expressed genes list. Moreover, we found that several intergroup specifically deregulated genes were involved in important biological processes and pathways, including B cell activation and Wnt signaling pathway. We conducted co-expression network using WGCNA and identified several hub genes that may play pivotal roles in MD resistance and tumorigenesis, e.g. CTLA4, SWAP70, CXCL12 and JCHAIN. According to the expression relationship between lncRNAs and MD resistance candidate mRNAs, five deregulated lncRNAs may implicate the chicken immunity by directly or indirectly regulating those hub genes. Conclusions: We profiled both lncRNA and mRNA expression patterns in MDV-infected chicken spleens. Expression variations of intergroup specifically deregulated genes engaged in important immune process likely contributed to robust immune system in the survivors. Some oncogenesis or MD resistance related genes deregulated between groups, like CTLA4, HDAC9 and CD72 were found. Co-expression network analysis manifested that lncRNAs may affect MD resistance and tumorigenesis in chicken spleens through their impact on expression of CTLA4, SWAP70 and some other genes that are critical in many important biological processes, such as B lymphocyte proliferation and activation.
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Project description:We infected mice with Brucella, took mouse spleens 6 days after infection, isolated and lysed mouse splenocytes for mass spectrometry experiments.
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Project description:To investigate gene expression profiles in susceptible spleens (SS) and resistant spleens (RS) from MDV-infected chickens and non-infected spleens (NS) from controls. Twelve spleens were chosen from three groups (four samples per group) to be used in chicken genome microarray to examine differential gene expression. In total, there were 4317 and 2593 differentially expressed (DE) genes in SS vs. NS and in SS vs. RS, respectively. However, no DE genes were found in RS vs. NS. The expression of twenty-four genes was verified by qPCR. In this study, we found weak, but detectable host immune response still existed in the late neoplastic transformation phase of MDV infection. Toll-like receptor pathway was affected in susceptible spleens compared to non-infected and resistant spleens. IL10 seemed to be exploited by virus to facilitate tumorigenesis. The expression of many members in insulin growth factor system was altered. IGFBP4 and IGFBP7 might be associated with MD lymphoma transformation. The expression profiles in resistant spleens were similar to those in non-infected spleens, which indicated most genes returned to baseline expression levels. Although latent MDV infection persists in resistant chicken for the whole life, it won’t interfere with normal function of genes.
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Project description:To investigate gene expression profiles in susceptible spleens (SS) and resistant spleens (RS) from MDV-infected chickens and non-infected spleens (NS) from controls. Twelve spleens were chosen from three groups (four samples per group) to be used in chicken genome microarray to examine differential gene expression. In total, there were 4317 and 2593 differentially expressed (DE) genes in SS vs. NS and in SS vs. RS, respectively. However, no DE genes were found in RS vs. NS. The expression of twenty-four genes was verified by qPCR. In this study, we found weak, but detectable host immune response still existed in the late neoplastic transformation phase of MDV infection. Toll-like receptor pathway was affected in susceptible spleens compared to non-infected and resistant spleens. IL10 seemed to be exploited by virus to facilitate tumorigenesis. The expression of many members in insulin growth factor system was altered. IGFBP4 and IGFBP7 might be associated with MD lymphoma transformation. The expression profiles in resistant spleens were similar to those in non-infected spleens, which indicated most genes returned to baseline expression levels. Although latent MDV infection persists in resistant chicken for the whole life, it wonM-bM-^@M-^Yt interfere with normal function of genes. Four susceptible spleens with tumors were obtained at 46-55 d.p.i., four resistant spleens were removed from survivors at 55-56 d.p.i. from MDV infected chickens, and four non-infected spleens were from controls at 40-56 d.p.i. Twelve one-color microarrays were utilized to detect differential gene expression among three groups.
2012-05-31 | E-GEOD-29805 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to investigate the differentially expressed miRNAs between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing. Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). RNA samples of three individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Hiseq 2500. Results: After raw data filtered, 12,150,275 and 15,227,930 reads of 18-32 bp, representing 569,847 and 543,062 unique sequences, were obtained for WRR- and WRR+ libraries, respectively. Through blasting with the chicken reference genome, 360,180 WRR- sequences and 327,391 WRR+ sequences, which accounted for more than 60% of the unique sequences, were perfectly matched.To analyze the miRNA detection efficiency of Illimuna deep sequencing, all the clean reads were blasted with the Rfam data base 10.1, annotated and then removed rRNA, tRNA, snoRNA and other snRNAs. The annotation results revealed that miRNAs accounted for more than 68% of all clean reads in the WRR− and WRR+ libraries. In this study, a total of 476 miRNAs were identified after compared the unique sequences against the chicken miRNAs precursors in miRBase 18.0. Base on unique sequences matched counts, 167 differential expression miRNAs were identified by DEGseq package using Benjamini-q-value of 0.001 as a cut-off. In ALV-J infected spleens, 83 miRNAs showed up-regulated expression and 84 were down-regulated when compared to uninfected samples. Conclusions: Our study represents the first time to analysis of miRNA Expression in Spleen of J Subgroup Avian Leukosis Virus (ALV-J) Infected (WRR+) and Uninfected (WRR-) Broilers. A total of 167 miRNAs were found to be differentially expressed in ALV-J infected spleens when compared to uninfected chickens. These miRNAs can be considered as candidates for further study ALV-J invasion.
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