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Series GSE83992 Query DataSets for GSE83992
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.
Overall design The wild type mouse testis RNAs were constructed NGS library by two different enzyme, then parallel sequenced in illumina Nextseq
Contributor(s) Tang C, Yu T, Yan W
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Submission date Jul 04, 2016
Last update date May 15, 2019
Contact name Wei Yan
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)
GSM2224951 AAspike-FFms-TT-SS1
GSM2224952 AAspike-FFms-TT-SS2
GSM2224953 AAspike-FFss-TT-SS1
BioProject PRJNA327756
SRA SRP077874

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83992_RAW.tar 1.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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