Suspect cases, bovine, to be filled
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB31779 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparative analysis of bovine, mouse and xenopus oocyte transcript profiles. The results from bovine and xenopus germinal vesicle stage oocytes in this experiment were compared to previously-published microarray data on preimplantation development in the mouse (Carter 2003).
2008-02-01 | E-MEXP-1339 | biostudies-arrayexpress
Project description:Bovine Immunodeficiency Virus (BIV) is a member of Retroviruses family which is natural pathogen of cattle, prevalent worldwide. The significance of BIV infection in cattle has not been clearly established and it is still unknown whether BIV induces a specific syndrome or whether it renders animals more susceptible to other infections. To gain insight into host response to BIV infection the pattern of gene expression in bovine macrophage cells (BoMac) was analyzed using BLO Plus microarrays from CAFG, Michigan State University ( GEO GPL9176).
2022-11-21 | GSE218260 | GEO
Project description:During mammalian pre-implantation embryonic development dramatic and orchestrated changes occur in gene transcription. The identification of the complete changes has not been possible until the development of the Next Generation Sequencing Technology. Here we report the first transcriptome dynamics of single matured bovine oocytes and all stages of pre-implantation embryos developed in vivo. Surprisingly, nearly half of the bovine genome, 11,488 to 12,729 genes involved in more than 100 pathways, is expressed in oocytes and early embryos. Despite the similarity in the total numbers of genes expressed across stages, the nature of the expressed genes is dramatically different. A total of 2,845 genes were differentially expressed among different stages, of which the largest change was observed between the 4- and 8-cell stages, demonstrating that the bovine embryonic genome activation occurs at this transition. Additionally, 774 genes were identified as only expressed/highly enriched in particular stages of development. Using weighted gene co-expression network analysis, we found 12 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified conserved key members (or hub genes) of the bovine expressed gene networks. Their vast association with other embryonic genes suggests that they may have important regulatory roles in embryogenesis; yet, the majority of the hub genes are relatively unknown/under-studied in embryos. We also conducted the first embryonic expression profile comparison across three mammalian species, human, mouse and bovine, for which RNA-seq data are available. We found that the three species share more maternally deposited genes than embryonic genome activated genes. More importantly, there are more similarities in embryonic transcriptomes between bovine and humans than between humans and mice, demonstrating that bovine embryos are better models for human embryonic development. This study provides the first comprehensive examination for gene activities in bovine embryos and identified little-known potential master regulators of pre-implantation development.
2014-09-10 | GSE59186 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs found to regulate several biological processes including adipogenesis. Understanding adipose tissue regulation is critical for beef cattle as fat is an important determinant of beef quality and nutrient value . This study analyzed the association between genomic context characteristics of miRNAs with their expression and function in bovine adipose tissue. Twenty-four subcutaneous adipose tissue biopsies were obtained from eight British-continental crossbred steers at 3 different time points . Total RNA was extracted and miRNAs were profiled using a miRNA microarray with expression further validated by qRT-PCR. A total of 224 miRNAs were detected of which 155 were expressed in all steers (n=8), and defined as the core miRNAs of bovine subcutaneous adipose tissue. Core adipose miRNAs varied in terms of genomic location (59.5% intergenic, 38.7% intronic, 1.2% exonic, and 0.6% mirtron), organization (55.5% non-clustered and 44.5% clustered), and conservation (49% highly conserved, 14% conserved and 37% poorly conserved). Clustered miRNAs and highly conserved miRNAs were more highly expressed (p<0.05) and had more predicted targets than non-clustered or less conserved miRNAs (p<0.001). A total of 34 miRNAs were coordinately expressed, being part of six identified relevant networks. Two intronic miRNAs (miR-33a and miR-1281) were shown to have coordinated expression with their host genes which are involved in lipid metabolism, suggesting these miRNAs may also play a role in regulation of lipid metabolism/adipogenesis of bovine adipose tissue. Furthermore, a total of 17 bovine specific miRNAs were predicted to be involved in the regulation of energy balance in adipose tissue. These findings improve our understanding on the behavior of miRNAs in the regulation of bovine adipogenesis and fat metabolism as it reveals that miRNA expression patterns and functions are associated with miRNA genomic organization and conservation in bovine adipose tissue.
2014-02-01 | GSE50489 | GEO
Project description:There are 19 differentially expressed microRNAs among new HIV-infected cases, old HIV-infected cases and healthy controls. Five microRNAs show trends in healthy controls, new HIV-infected cases and old HIV-infected cases, they are hsa-miR-1291, and hsa-miR-3609 with up-trends, and hsa-miR-3162-3p, hsa-miR-874-5p and hsa-miR-4258 with down-trends.
2017-12-01 | GSE103555 | GEO
Project description:Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC). Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases and additional 70 ESCC cases were subjected to array comparative genomic hybridization (a-CGH) analysis.
2014-03-11 | GSE54994 | GEO
Project description:Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC). Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases and additional 70 ESCC cases were subjected to array comparative genomic hybridization (a-CGH) analysis.
2014-03-11 | GSE54993 | GEO