Circular RNAs expression profiles in canine mammary tumours
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA573536 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10160737_1.fastq.gz | Fastqsanger.gz | |||
| SRR10160737_2.fastq.gz | Fastqsanger.gz | |||
| SRR10160738_1.fastq.gz | Fastqsanger.gz | |||
| SRR10160738_2.fastq.gz | Fastqsanger.gz | |||
| SRR10160739_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:We explored the expression profile of circRNAs in canine mammary tumours using high-throughput sequencing technology. In our study, we analysed the expression profiles of 3 pairs of canine mammary tumours and their adjacent normal tissues. The total RNA was extracted, and a RNA library was constructed. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses revealed that these genes were mainly concentrated in 14 biological pathways. We selected 11 validated circRNAs and further confirmed the existence of these circRNAs by qRT-PCR. The circRNA-miRNA network diagram was constructed by using Cytoscape software. We found a total of 14851 circRNAs and 106 differentially expressed circRNAs in canine mammary tumours and their adjacent normal tissues (fold change ≥ 2, P ≤ 0.05). There were 64 upregulated circRNAs and 42 downregulated circRNAs. The main GO functions were the regulation of the regulated secretory pathway, the regulation of neurotransmitter secretion and the positive regulation of phagocytosis. Most of these pathways were related to the cGMP-PKG (cyclic guanosine monophosphate) signalling pathway, the cAMP (cyclic adenosine monophosphate) signalling pathway and the OXYTOCIN signalling pathway. CircRNAs have the function of adsorbing miRNA, similar to a sponge, and we further constructed the interaction network of circRNAs and miRNAs. The screened source genes closely related to canine mammary tumours included RYR2, PDE4D, ROCK2, CREB3L2 and UBA3. The screened circRNAs related to canine mammary tumours included chr27:26618544-26687235-, chr26:8194880-8201833+, and chr17:7960861-7967766-.In conclusion, our study uncovered circRNA expression profiles in canine mammary tumours. Moreover, some circRNAs may be used as potential biomarkers for screening dogs with high-risk canine mammary tumours.
2019-09-23 | GSE137825 | GEO
Project description:Molecular mechanisms of the canine mammary malignancy. RNA isolated from canine mammary tumours of the 3rd grade of malignancy was pooled and hybrydized on the same microarray as RNA isolated from canine mammary tumours of the 1st grade of malignancy. Based on the results the "malignancy portrait" was assessed.
2013-10-01 | GSE44033 | GEO
Project description:Molecular mechanisms of the canine mammary malignancy. RNA isolated from canine mammary tumours of the 3rd grade of malignancy was pooled and hybrydized on the same microarray as RNA isolated from canine mammary tumours of the 1st grade of malignancy. Based on the results the "malignancy portrait" was assessed. Dye-swap experiment, gene expression in the most malignant canine mammary tumours (the 3rd grade of malignancy) was compared to the less malignant tumours (1st grade of malignancy).
2013-10-01 | E-GEOD-44033 | biostudies-arrayexpress
Project description:In this study, the proteins found in extracellular vesicles of different cells relevant in canine mammary tumours (CMTs) research were investigated to identify CMT subtype specific proteome signatures.
2024-11-07 | PXD046033 | Pride
Project description:Genome-wide analysis identifies germ-line risk factors associated with canine mammary tumours
| PRJEB13624 | ENA
Project description:Spontaneous mammary tumours are the most prevalent type of neoplasm in women as well as in female dogs. Even though ovarian hormones, mainly estrogens and progestins, are known to play a key role in mammary tumorigenesis, conflicting reports have been obtained from in vivo and in vitro studies concerning their role, especially of progestins, in mammary tumorigenesis. Prolonged exposure to high levels of progestins during unusually long luteal phase of oestrous cycle is suspected to be the key event in canine mammary tumorigenesis. Accordingly, our previous studies have shown development of mammary hyperplasia in dogs upon prolonged progestin administration. In this study, we used canine cDNA microarrays to identify oncogenic determinants in progestin-induced canine hyperplasia (CMH) and spontaneous tumours (CMC) by comparing them to normal tissue. CMH profile indicated amplification of genes involved in cell proliferation, like PCNA, NPY and RAN, and also alterations in expression of transcription factors and cell adhesion molecules. In addition to amplified cell proliferation signature, CMC profile also identified major alterations in expressions of genes involved in cell motility, cytoskeletal organization and extracellular components. Overall, gene expression profile of CMH indicated an advantage for cell proliferation, whereas that of CMC indicated an advantage for proliferation as well as neoclassic transformation. In conclusion, our findings indicate strong oncogenic potential of progestins in canine mammary gland. In addition, CMC gene expression profile greatly contribute to the identification of their molecular abnormalities and may facilitate the identification of new therapeutic targets. Keywords: Expression profiling by using cDNA microarray
2009-02-09 | GSE13754 | GEO
Project description:Purpose: A novel member of RNAs, circular RNAs (circRNAs), has recently been evidenced to play key role on biological process regulation. However, the global landscape of circular RNA remains largely unknown. In the present study, deep RNA-sequencing technique was employed to identify and characterize the circular RNAs expressed in lactating rat mammary gland.compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods:Deep RNA-sequencing technique was employed Results: A total of 6824 and 4523 circRNAs were identified from rat mammary glands at two lactation stages, respectively. Numerous circRNAs seem to be specifically expressed in different lactation stages, as only 1314 circRNAs were detected in both libraries. Majority of the candidate circRNAs maps to intronic and intergenic regions, namely noncoding regions. There existed the circular preference or specificity of some genes. Interestingly, 4 protein coding genes (Rev3l, IGSF11, MAML2, and LPP) that also tanscripted high level circRNAs have been reported to be involved in cancer. The distribution of specific miRNA binding sites and RNA binding proteins binding sites also implied the role of circRNAs in mammary gland development and tumorigenesis. Conclusions:The results provide the basis for comparisons with breast cancer profiles and for selection of representative circRNA candidates for future functional characterization in breast development and breast cancer.
2017-08-20 | GSE60539 | GEO
Project description:[original title] Metastatic Canine Mammary Carcinomas can be Identified by a Gene Expression Profile that partly Overlaps with Human Breast Cancer Profiles. Introduction: Similar to human breast cancer mammary tumors of the female dog are commonly associated with a fatal outcome due to the development of distant metastases. However, the molecular defects leading to metastasis are largely unknown and the value of canine mammary carcinoma as a model for human breast cancer is unclear. In this study, we analyzed the gene expression signatures associated with mammary tumor metastasis and asked for parallels with the human equivalent. Methods: Messenger RNA expression profiles of twenty-seven lymph node metastasis positive or negative canine mammary carcinomas were established by microarray analysis. Differentially expressed genes were functionally characterized and associated with molecular pathways. The findings were also correlated with published data on human breast cancer. Results: Metastatic canine mammary carcinomas had 1,011 significantly differentially expressed genes when compared to non-metastatic carcinomas. Metastatic carcinomas had a significant up-regulation of genes associated with cell cycle regulation, matrix modulation, protein folding and proteasomal degradation whereas cell differentiation genes, growth factor pathway genes and regulators of actin organization were significantly down-regulated. Interestingly, 265 of the 1,011 differentially expressed canine genes are also related to human breast cancer and, vice versa, parts of a human prognostic gene signature were identified in the expression profiles of the metastatic canine tumors. Conclusions: Metastatic canine mammary carcinomas can be discriminated from non-metastatic carcinomas by their gene expression profiles. More than one third of the differentially expressed genes are also described of relevance for human breast cancer. Many of the differentially expressed genes are linked to functions and pathways which appear to be relevant for the induction and maintenance of metastatic progression and may represent new therapeutic targets. Furthermore, dogs are in some aspects suitable as a translational model for human breast tumors in order to identify prognostic molecular signatures and potential therapeutic targets.
2010-12-01 | GSE20718 | GEO
Project description:Circular RNAs (circRNAs) are widespread circular forms of non-coding RNAs with largely unknown function. Because stimulation of mammary cells with the epidermal growth factor (EGF) leads to dynamic changes in the abundance of both coding and non-coding RNA molecules, and culminates in the acquisition of a robust migratory phenotype, this cellular model might disclose functions of circRNAs. Here we show that circRNAs of EGF-stimulated mammary cells are stably expressed, while mRNAs and micro-RNAs change within minutes. In general, the circRNAs we detected are relatively long-lived and weakly expressed. Interestingly, they are almost ubiquitously co-expressed with the corresponding linear transcripts, and the respective, shared promoter regions are more active compared to genes producing linear isoforms only. These findings imply that altered abundance of circRNAs, unlike changes in the levels of other RNAs, might not play critical roles in signaling cascades and downstream transcriptional networks that rapidly commit cells to specific outcomes. Detection of circRNAs from RNA-Seq â triplicate
2015-12-17 | E-GEOD-71195 | biostudies-arrayexpress
Project description:Circular RNAs (circRNAs) are widespread circular forms of non-coding RNAs with largely unknown function. Because stimulation of mammary cells with the epidermal growth factor (EGF) leads to dynamic changes in the abundance of both coding and non-coding RNA molecules, and culminates in the acquisition of a robust migratory phenotype, this cellular model might disclose functions of circRNAs. Here we show that circRNAs of EGF-stimulated mammary cells are stably expressed, while mRNAs and micro-RNAs change within minutes. In general, the circRNAs we detected are relatively long-lived and weakly expressed. Interestingly, they are almost ubiquitously co-expressed with the corresponding linear transcripts, and the respective, shared promoter regions are more active compared to genes producing linear isoforms only. These findings imply that altered abundance of circRNAs, unlike changes in the levels of other RNAs, might not play critical roles in signaling cascades and downstream transcriptional networks that rapidly commit cells to specific outcomes. Histone 3 Lysine 27 Acetylation â 2 replicates
2015-12-17 | E-GEOD-71196 | biostudies-arrayexpress