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PROVIDER: PRJEB59217 | ENA |
REPOSITORIES: ENA
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Project description:Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose. We identified over 470 candidate CNV regions (CNVRs) in Bos B. taurus/B. indicus; 118 candidate CNV regions (CNVRs) in B. grunniens, 139 CNVRs in B. bubalis. Furthermore, based on the Y haplotypes of B. taurus/ B. indicus, Wwe also identified 69, 337, and 251 candidate CNV regions (CNVRs) in the sub-groups of Y1, Y2 and Y3 haplotypes.
2014-12-30 | GSE47086 | GEO
Project description:Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp - 4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst=0.440) and STUB1 (Fst=0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst=0.222) and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.
2020-02-21 | GSE142218 | GEO
Project description:Comparative microarray analysis of Rhipicephalus (Boophilus) microplus expression profiles of larvae pre-attachment and feeding adult female stages on Bos indicus and B. taurus cattle Global analysis of gene expression changes in R. microplus during larval, pre-attachment and early adult stages of its life cycle feeding on Bos indicus and Bos taurus cattle were compared using gene expression microarray analysis. Among the 13 601 R. microplus transcripts from BmiGI Version 2 we identified 297 up and 17 down regulated transcripts were differentially expressed between R. microplus feeding on tick resistant cattle [Bos indicus (Brahman)] compared to R. microplus feeding on tick susceptible cattle [Bos taurus (Holstein-Friesian)]. These include genes encoding enzymes involved in primary metabolism, and genes related to stress, defence, cell wall modification, cellular signaling, receptor and cuticle. Microarrays were validated by qRT-PCR analysis of selected transcripts including the validation of three housekeeping genes. The analysis of all tick stages under survey suggested a coordinated regulation of defence proteins, proteases, and protease inhibitors to achieve successful attachment and survival of R. microplus on different host breeds particularly Bos indicus cattle. The microarray was conducted by NimbleGen Systems Inc following the method reported by Saldivar [Saldivar L et al., Insect Mol Biol 2008, 17(6):597-606]. 10 samples: 2 larva, 2 pre-attachment larva in B. indicus and 2 in B. taurus, and 2 adult ticks in B. indicus and 2 in B. taurus
2010-07-09 | E-GEOD-20605 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE13852: Expression profiling of Bos taurus lymph nodes upon infection with Ovine Herpesvirus 2 GSE13853: Expression profiling of Ovine Herpesvirus 2-infected lymph nodes from Bos taurus Refer to individual Series
2010-05-15 | E-GEOD-13854 | biostudies-arrayexpress
Project description:Transciprional profiling of horn forming region of Bos taurus comparing horned, polled and scurred cattle.
2010-05-01 | GSE21585 | GEO
Project description:Comparative microarray analysis of Rhipicephalus (Boophilus) microplus expression profiles of larvae pre-attachment and feeding adult female stages on Bos indicus and B. taurus cattle Global analysis of gene expression changes in R. microplus during larval, pre-attachment and early adult stages of its life cycle feeding on Bos indicus and Bos taurus cattle were compared using gene expression microarray analysis. Among the 13 601 R. microplus transcripts from BmiGI Version 2 we identified 297 up and 17 down regulated transcripts were differentially expressed between R. microplus feeding on tick resistant cattle [Bos indicus (Brahman)] compared to R. microplus feeding on tick susceptible cattle [Bos taurus (Holstein-Friesian)]. These include genes encoding enzymes involved in primary metabolism, and genes related to stress, defence, cell wall modification, cellular signaling, receptor and cuticle. Microarrays were validated by qRT-PCR analysis of selected transcripts including the validation of three housekeeping genes. The analysis of all tick stages under survey suggested a coordinated regulation of defence proteins, proteases, and protease inhibitors to achieve successful attachment and survival of R. microplus on different host breeds particularly Bos indicus cattle.
2010-07-09 | GSE20605 | GEO
Project description:Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 genes have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ~105 Bos taurus indicus X Bos taurus taurus F1 conceptuses using RNA sequencing. For this, we developed a bioinformatics pipeline to identify parental-specific SNPs after filtering A-to-I RNA editing sites. We identified 53 genes subject to monoallelic expression. A total of 23 are genes known to be imprinted in the cow and 7 are previously-characterized imprinted genes in human and/or mouse that have not be reported to be imprinted in cattle. Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinting clusters, whereas the other 13 genes are distributed across the bovine genome and not close to any known imprinting clusters. To exclude potential cis-eQTL effects on allelic expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus X Bos taurus taurus F1s and identified eight novel imprinted genes in bovine. Further, we identified 671 candidate A-to-I RNA editing sites and describe imprinted X inactivation in the bovine trophectoderm-derived CT1 cell line. Our results expand the imprinted gene list in bovine and demonstrate that monoallelic gene expression can be the result of cis-eQTL effect.
2016-08-17 | GSE77389 | GEO
Project description:Purpose: The goal of this study was to use NGS RNAseq to compare transcriptomic profiles of bovine leucocytes from different host genotypes when infected with the pathogenic apicomplexan parasite T. annulata with a view to elucidating mechanisms associated with in vivo virulence between Bos taurus and Bos indicus cattle. Methods: infected cell lines were generated from in vivo infections of cows with T. annulata. 5 were derived from Bos taurus hosts and 6 were derived from Bos indicus hosts. We extracted RNA from each immortlaized cell line and generated paired end reads using XXXXXX. Paired end reads were trimmed (Cudadapt 1.2.1 abd Sickle version 1.2) , and aligned to the Bos taurus genome (UMD3.1) using Bowtie 2. Differential analysis was performed useing DEseq 2. qRT PCR was used for validation on a subset of 18 genes using SYBR green. Results: We found a total of 2022 differentially expressed genes (p < 0.05) using DEseq2, and many of these genes are involved in pathways implicated in in vivo differences in virulence observed between host genotypes, including i genes onvolved in interferon pathways, the innate immune response, or cancer-asscoiated.
2021-06-30 | GSE159268 | GEO