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| Status |
Public on Jul 05, 2016 |
| Title |
An improved method for identifying biological circular RNAs |
| Organisms |
Mus musculus; synthetic construct |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: We are using the illumina sequencing to compare the false positive and true positive circular RNA findings to confine the method to detect the true circular RNAs
Methods: The testis whole transcriptome profiling was generated from 4-week mouse testis using illumina Nextseq, duplicated. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: our data suggest that circular RNAs identified based on junction sequences in the RNA-seq reads, especially those from Illumina Hiseq sequencing, mostly result from template-switching events during reverse transcription by MMLV-derived reverse transcriptases. It is critical to employ reverse transcriptases lacking terminal transferase activity (e.g., MonsterScript) to construct sequencing library or perform RT-PCR for identification and quantification of true circular RNAs.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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| |
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| Overall design |
The wild type mouse testis RNAs were constructed NGS library by two different enzyme, then parallel sequenced in illumina Nextseq
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| Contributor(s) |
Tang C, Yu T, Yan W |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jul 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Yan |
| E-mail(s) |
wyan@medicine.nevada.edu
|
| Phone |
(775) 784-7765
|
| Organization name |
University of Nevada
|
| Department |
Physiology
|
| Lab |
Wei Yan Lab
|
| Street address |
1664 N. Virginia Street
|
| City |
reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
|
| Samples (12)
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| Relations |
| BioProject |
PRJNA327756 |
| SRA |
SRP077874 |
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