GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE162152 Query DataSets for GSE162152
Status Public on Sep 21, 2021
Title Identification and evolutionary comparison of circular RNAs in five mammalian species and three organs.
Organisms Macaca mulatta; Homo sapiens; Mus musculus; Rattus norvegicus; Monodelphis domestica
Experiment type Expression profiling by high throughput sequencing
Summary Circular RNAs (circRNAs) are found across eukaryotes and can function in post-transcriptional gene regulation. Their biogenesis through a circle-forming backsplicing reaction is facilitated by reverse-complementary repetitive sequences promoting pre-mRNA folding. Orthologous genes from which circRNAs arise overall, contain more strongly conserved splice sites and exons than other genes, yet it remains unclear to what extent this conservation reflects purifying selection acting on the circRNAs themselves.
Our analyses of circRNA repertoires across five species representing three mammalian lineages (marsupials, eutherians: rodents, primates) reveal that surprisingly few circRNAs arise from orthologous genes from different species. Even the circRNAs from shared loci are associated with young, recently active and species-specific transposable elements, rather than with common, ancient transposon integration events. These observations suggest that many circRNAs emerged convergently during evolution – as a byproduct of splicing in orthologs prone to transposable element insertion. Overall, our findings argue against widespread functional circRNA conservation.
Overall design Annotation and expression analyses of circRNAs using RNA-sequencing data in five mammalian species (opossum, mouse, rat, rhesus macaque, human) and three organs (liver, cerebellum, testis). Included are three biological replicates for each condition (conditions = species and tissues). All organisms used were male and wild type. Each replicate was splitted into two: the first sample was directly used for library preparation, the second one treated with RNase R prior library preparation to degrade linear RNAs, which subsequently enrichs circRNAs. Samples were sequenced using Illumina paired-end sequencing and circRNAs annotated and analysed for their evolutionary history.
Web link
Contributor(s) Gruhl F, Janich P, Kaessmann H, Gatfield D
Citation(s) 34542406
Submission date Nov 25, 2020
Last update date Jan 04, 2022
Contact name Franziska Gruhl
Organization name SIB Swiss Institute of Bioinformatics
Street address University of Lausanne, Quartier Sorge
City Lausanne
ZIP/Postal code 1015
Country Switzerland
Platforms (5)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18694 Illumina HiSeq 2500 (Rattus norvegicus)
Samples (84)
GSM4943498 comd_lv1
GSM4943499 comd_lv2
GSM4943500 comd_lv3
BioProject PRJNA680762
SRA SRP294141

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
GSE162152_hsCircRNA_cpms.txt.gz 141.6 Kb (ftp)(http) TXT
GSE162152_hsCircRNAs.gtf.gz 385.7 Kb (ftp)(http) GTF
GSE162152_mdCircRNA_cpms.txt.gz 51.5 Kb (ftp)(http) TXT
GSE162152_mdCircRNAs.gtf.gz 120.8 Kb (ftp)(http) GTF
GSE162152_mmCircRNA_cpms.txt.gz 49.7 Kb (ftp)(http) TXT
GSE162152_mmCircRNAs.gtf.gz 128.2 Kb (ftp)(http) GTF
GSE162152_rmCircRNA_cpms.txt.gz 113.0 Kb (ftp)(http) TXT
GSE162152_rmCircRNAs.gtf.gz 279.9 Kb (ftp)(http) GTF
GSE162152_rnCircRNA_cpms.txt.gz 67.2 Kb (ftp)(http) TXT
GSE162152_rnCircRNAs.gtf.gz 176.1 Kb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap