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Series GSE28888 Query DataSets for GSE28888
Status Public on Apr 05, 2012
Title Effects of ADARs on small RNA processing pathways in C. elegans
Organism Caenorhabditis elegans
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine to inosine in double-stranded RNA (dsRNA). To evaluate effects of ADARs on small RNAs that derive from dsRNA precursors, we performed deep-sequencing, comparing small RNAs from wildtype and ADAR mutant C. elegans. While editing in small RNAs was rare, at least 40% of microRNAs had altered levels in at least one ADAR mutant strain, and miRNAs with significantly altered levels had mRNA targets with correspondingly affected levels. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also had altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. The 26G class of endo-siRNAs was significantly affected by ADARs, and many altered 26G loci had intronic reads, and histone modifications associated with transcriptional silencing. Our data indicate ADARs, through both direct and indirect mechanisms, are important for maintaining wildtype levels of many small RNAs in C. elegans.
 
Overall design Deep sequencing of small RNAs in wild-type (N2), adr-1 null, adr-2 null and adr-1;adr-2 null mixed stage C. elegans
 
Contributor(s) Warf MB, Johnson WE, Bass BL
Citation(s) 22673872
Submission date Apr 27, 2011
Last update date May 15, 2019
Contact name Michael Bryan Warf
E-mail(s) warf@biochem.utah.edu
Phone 801-585-3110
Organization name University of Utah
Department Biochemistry
Lab Brenda Bass
Street address 15 N Medical Dr East, room 4800
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
 
Platforms (1)
GPL9269 Illumina Genome Analyzer II (Caenorhabditis elegans)
Samples (5)
GSM715830 Wild-type small RNAs Sample 1
GSM715831 Wild-type small RNAs Sample 2
GSM715832 adr-1 mutant small RNAs
Relations
SRA SRP006489
BioProject PRJNA140639

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

Supplementary file Size Download File type/resource
GSE28888_RAW.tar 621.3 Mb (http)(custom) TAR (of TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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