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RNA sequencing of brain and cerebellum samples from MTCL1 mutant and control animals in cattle and mouse

ABSTRACT: RNAseq of MTCL1 mutant and control animals in cattle and mouse

PROVIDER: PRJEB59267 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10807500_1.fastq.gz	Fastqsanger.gz
	ERR10807500_2.fastq.gz	Fastqsanger.gz
	ERR10807501_1.fastq.gz	Fastqsanger.gz
	ERR10807501_2.fastq.gz	Fastqsanger.gz
	ERR10807502_1.fastq.gz	Fastqsanger.gz

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RNA sequencing of brain and cerebellum samples from MTCL1 mutant and control animals in cattle and mouse

Project description:RNAseq of MTCL1 mutant and control animals in cattle and mouse

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Combinatorial discriminant analysis applied to RNAseq data reveals a set of 10 transcripts as signatures of infection of cattle with Mycobacterium avium subsp. Paratuberculosis (MAP).

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Comparison of Mycobacterium bovis-infected cattle versus control non-infected cattle using the BOTL-5 microarray

Project description:Background: Bovine tuberculosis is an enduring disease of cattle that has significant repercussions for human health. The advent of high-throughput functional genomics technologies has facilitated large-scale analyses of the immune response to this disease that will ultimately lead to novel diagnostics and therapeutic targets. Analysis of mRNA abundance in peripheral blood mononuclear cells (PBMC) from six Mycobacterium bovis infected cattle and six non-infected controls was performed. A targeted immunospecific bovine cDNA microarray with duplicated spot features representing 1,391 genes was used to test the hypothesis that a novel gene expression profile may exist in M. bovis infected animals in vivo. Results: In total, 378 gene features were differentially expressed at the P ≤ 0.05 level in bovine tuberculosis (BTB)-infected and control animals, of which 244 were expressed at lower levels (65%) in the infected group. Lower relative expression of key innate immune genes such as the Toll-like receptor 2 (TLR2) and TLR4 genes, lack of differential expression of indicator adaptive immune gene transcripts (IFNG, IL2, IL4), and lower BOLA major histocompatability complex – class I (BOLA) and class II (BOLA-DRA) gene expression was consistent with innate immune gene repression in the BTB-infected animals. Supervised hierarchical cluster analysis and class prediction validation identified a panel of 15 genes predictive of disease status and selected gene transcripts were validated (n = 8 per group) by real time quantitative reverse transcription PCR. Conclusion: These results suggest that large-scale expression profiling can identify gene signatures of disease in peripheral blood that can be used to classify animals on the basis of in vivo infection, in the absence of exogenous antigenic stimulation. Keywords: Disease state analysis

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Targeted Transcriptome Analysis of Beef Cattle Persistently Infected with Bovine Viral Diarrhea Virus

Project description:Bovine Viral Diarrhea Virus (BVDV) is an endemic virus of North American cattle populations with significant economic and animal health impacts. While BVDV infection has a myriad of clinical manifestations, a unique and problematic outcome is the establishment of a persistently infected (PI) animal following in-utero viral infection. While it is well established that PI animals serve as a constant reservoir of BVDV, the mechanism for the maintained infection remains unknown despite multiple theories. The purpose of this study was to use transcriptome analysis to further define long term immune status of adult PI cattle and offer insight into the potential mechanistic establishment of persistent BVDV infection, in utero. Peripheral blood mononuclear cells were collected from PI beef cattle (N=6) and uninfected controls (N=6) for targeted RNAseq analysis conducted using 54 genes of interest and followed by pathway enrichment analysis. Analysis revealed 29 differentially expressed genes (FDR < 0.05, fold change > 2) representing 14 significant KEGG pathways between PI and control animals (FDR < 0.05). Transcriptome changes indicate chronic upregulation of interferon gamma (IFNG) with unexpected expression of related genes, suggesting a maintained stimulation of the PI immune system resulting in virus-mediated dysregulation of immune function.

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Analysis of copy number variations among diverse cattle breeds

Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.

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