Project description: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. The wild type mouse testis RNAs were constructed NGS library by two different enzyme, then parallel sequenced in illumina Nextseq

2016-07-05 | E-GEOD-83992 | biostudies-arrayexpress

Homo sapiens

Project description:Circular RNAs are a large class of animal RNAs with regulatory potency (RNA-Seq)

| PRJNA186745 | ENA

Homo sapiens

Project description:Identification of Senescence-Associated Circular RNAs (SAC-RNAs) reveals senescence suppressor CircPVT1

| PRJNA339301 | ENA

Homo sapiens

Project description:Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood

| PRJNA297345 | ENA

Homo sapiens

Project description:Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer

| PRJNA742821 | ENA

Small RNA sequencing of the 8 to 30-nucleotide window in homo sapiens

Project description:RNA-sequencing (RNA-Seq) protocols and bioinformatic pipelines are designed to streamline downstream analyses on sequences believed to be the most important. Here, we have challenged this dogma by preserving ribosomal RNA (rRNA) in our samples and by lowering the minimal RNA size window of our small RNA-Seq analyses to 8 nt

2022-09-01 | GSE179678 | GEO