NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE89765 Query DataSets for GSE89765
Status Public on Feb 23, 2018
Title ADARs regulate small RNAs mapped to edited sequences
Sample organism Caenorhabditis elegans
Experiment type Non-coding RNA profiling by high throughput sequencing
Third-party reanalysis
Summary Cellular RNAs containing double-stranded RNA (dsRNA) structures are subject to A-to-I RNA editing by the adenosine deaminases that act on RNA (ADARs). While A-to-I editing can alter mRNA coding potential, most editing is observed in non-coding sequences, the function of which remains poorly characterized. To correlate small RNA population with expression patterns of ADARs and hyperedited RNAs (editing-enriched regions: EERs) defined and characterized in a separate RNAseq analysis, we re-analyzed existing smallRNAseq datasets of a wildtype strain and a strain lacking ADARs (adr-1;adr-2). Analysis of primary siRNAs from mixed-stage worms revealed that ADARs impact siRNA biogenesis from EERs. We then analyzed primary and secondary RNAs mapping to EERs from embryo-stage or L4-stage worms and observed that ADAR effects on siRNA levels are dependent on developmental stage.
 
Overall design For mixed-stage wildtype (N2) and adr-1;adr-2 samples, small RNAs with 5' monophosphates sequenced on Illumina HiSeq2000 (see GSE28888) were mapped to 1523 EERs defined in GSE79375, excluding those mapping to annotated miRNA or 21U-RNA loci. For embryo and L4-staged samples (from PMID: 21909095), small RNAseq using 5'phosphate independent protocols were likewise mapped to 1523 EERs, excluding those mapping to annotated miRNA or 21U-RNA loci.

This series includes two samples re-analyzed from GSE28888 and eight samples re-analyzed from PubMed ID 21909095. These eight samples from PubMed ID 21909095 have not been deposited in GEO or SRA or any other public database and were obtained upon request from the authors. Included on this record are alignment files of reads aligned to EERs (in SAM format) and processed data for all re-analyzed samples.
 
Contributor(s) Reich DP, Tyc KM, Bass BL
Citation(s)
  • Reich DP, Tyc KM, Bass BL. C. elegans ADARs antagonize silencing of cellular dsRNAs by the antiviral RNAi pathway. Genes Dev 2018 Feb 1;32(3-4):271-282. PMID: 29483152
Submission date Nov 10, 2016
Last update date Feb 28, 2018
Contact name Brenda L Bass
E-mail(s) bbass@biochem.utah.edu
Phone 8015814884
Organization name University of Utah
Department Biochemistry
Lab Brenda Bass
Street address 15 N Medical Drive East, Rm 4800
City Salt Lake City
State/province Utah
ZIP/Postal code 84112-5650
Country USA
 
This SubSeries is part of SuperSeries:
GSE89890 Gene regulation by small RNAs and ADAR RNA editing
Relations
Reanalysis of GSM715830
Reanalysis of GSM715834
BioProject PRJNA353119

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
GSE89765_5dep_sense_EER_sRNA_RPM.txt.gz 22.1 Kb (ftp)(http) TXT
GSE89765_5ind_antisense_EERs_sRNA_RPM.txt.gz 45.4 Kb (ftp)(http) TXT
GSE89765_metadata_and_file_description.xls.gz 8.4 Kb (ftp)(http) XLS
GSE89765_sam_files.tar.gz 23.5 Mb (ftp)(http) TAR
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.