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Series GSE60539 Query DataSets for GSE60539
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
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 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.
Overall design The rat mammary glands at different lactation stages were investigated
Contributor(s) Zhang C, Wang Y
Citation(s) 26472973
Submission date Aug 20, 2014
Last update date May 15, 2019
Contact name Yanhong Wang
Organization name Jiangsu Normal University
Street address shanghai road number101
City Xuzhou
ZIP/Postal code 221116
Country China
Platforms (1)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (4)
GSM1481815 Day1 Rnase R
GSM1481816 Day1 mock
GSM1481817 Day7 Rnase R
BioProject PRJNA258577
SRA SRP045658

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Supplementary file Size Download File type/resource
GSE60539_RAW.tar 2.2 Mb (http)(custom) TAR (of XLSX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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