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Series GSE60851 Query DataSets for GSE60851
Status Public on Apr 23, 2017
Title Analysis of canonical A-to-I RNA editing in Drosophila using ICE-seq
Organisms Drosophila melanogaster; Drosophila yakuba
Experiment type Expression profiling by high throughput sequencing
Other
Summary The predominant form of RNA editing in animals is the enzymatic conversion of adenosine to inosine that is sequenced in cDNA as guanine. While RNA editing should be identifiable from RNA-seq data alone, genomic SNPs as well as sequencing and mapping errors result in a high false-positive rate. We used Inosine Chemical Erasing (ICE) with deep sequencing (ICE-seq) in order to validate A-to-I RNA editing genome-wide without the need for the sequencing of the underlying genomic DNA. We called RNA editing events in the head transcriptome of the reference strain of Drosophila melanogaster and six resequenced strains of Drosophila yakuba using the Illumina HiSeq and NextSeq platforms. We compared RNA editing sites reported in other studies and measured the level of conservation between D. melanogaster and D. yakuba. We found that while some of the best-studied editing sites in D. melanogaster are also edited in D. yakuba, we also detect a significant amount of species-specific editing in genes with different Gene Ontology enrichments, which suggests that the biological function of RNA editing in the two Drosophila species is diverging.
 
Overall design ICE-seq and RNA-seq pairs were generated for 6 strains of Drosophila yakuba and two replicates of Drosophila melanogaster. Two additional RNA-seq libraries were generated on the HiSeq and NextSeq.
 
Contributor(s) Park E, Rogers R, Andolfatto P, Thornton K, Mortazavi A
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Submission date Aug 27, 2014
Last update date May 15, 2019
Contact name Eddie Park
E-mail(s) eddiep@uci.edu
Phone 9498248393
Organization name UCI
Department DevCell
Lab Mortazavi
Street address 2300 Biological Sciences 3
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platforms (3)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
GPL19131 Illumina NextSeq 500 (Drosophila yakuba)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (20)
GSM1490016 CY08_ICE
GSM1490017 CY21B3_ICE
GSM1490018 NY48_ICE
Relations
BioProject PRJNA259668
SRA SRP045838

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

Supplementary file Size Download File type/resource
GSE60851_Dmel_RNA_HiSeq_R1.txt.gz 468.0 Kb (ftp)(http) TXT
GSE60851_Dmel_RNA_HiSeq_R2.txt.gz 799.5 Kb (ftp)(http) TXT
GSE60851_Dmel_RNA_NextSeq_R1.txt.gz 1.5 Mb (ftp)(http) TXT
GSE60851_Dmel_RNA_NextSeq_R2.txt.gz 3.7 Mb (ftp)(http) TXT
GSE60851_dmel.bed.gz 7.2 Kb (ftp)(http) BED
GSE60851_dyak.bed.gz 7.6 Kb (ftp)(http) BED
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