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| Status |
Public on Aug 20, 2017 |
| Title |
Identify and characterize the circular RNAs expressed in lactating rat mammary glands |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
The rat mammary glands at different lactation stages were investigated
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| Contributor(s) |
Zhang C, Wang Y |
| Citation(s) |
26472973 |
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| Submission date |
Aug 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yanhong Wang |
| E-mail(s) |
7096871@163.com
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| Organization name |
Jiangsu Normal University
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| Street address |
shanghai road number101
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| City |
Xuzhou |
| ZIP/Postal code |
221116 |
| Country |
China |
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| Platforms (1) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA258577 |
| SRA |
SRP045658 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60539_RAW.tar |
2.2 Mb |
(http)(custom) |
TAR (of XLSX) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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