Dataset mE_A-to-I_RNA_Editing_Sites

General Information
Name	mE_A-to-I_RNA_Editing_Sites	Species	D. melanogaster
Dataset type	RNA-Seq transcriptome A-to-I RNA editing sites	FlyBase ID	FBlc0000259
Source & Content
Consists of	cDNA short sequencing reads from high-throughput sequencing, sites of A-to-I RNA editing only. (Graveley et al., 2011)
Created by
Available from
Strain	iso-1 (Graveley et al., 2011)
Stage & tissue

Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	RNA A-to-I editing sites as determined from short sequencing reads of cDNA prepared from 30 different developmental stages. The frequency of editing at each site throughout development is analyzed and the effects of editing on the amino acids encoded are predicted. (Graveley et al., 2011)
Parent collections	modENCODE_mRNA-Seq_U
Component collection(s)	mE_mRNA_em0-2hr_A-to-I_RNA_Editing_Sites mE_mRNA_em2-4hr_A-to-I_RNA_Editing_Sites mE_mRNA_em4-6hr_A-to-I_RNA_Editing_Sites mE_mRNA_em6-8hr_A-to-I_RNA_Editing_Sites mE_mRNA_em8-10hr_A-to-I_RNA_Editing_Sites mE_mRNA_em10-12hr_A-to-I_RNA_Editing_Sites mE_mRNA_em12-14hr_A-to-I_RNA_Editing_Sites mE_mRNA_em14-16hr_A-to-I_RNA_Editing_Sites mE_mRNA_em16-18hr_A-to-I_RNA_Editing_Sites mE_mRNA_em18-20hr_A-to-I_RNA_Editing_Sites mE_mRNA_em20-22hr_A-to-I_RNA_Editing_Sites mE_mRNA_em22-24hr_A-to-I_RNA_Editing_Sites mE_mRNA_L1_A-to-I_RNA_Editing_Sites mE_mRNA_L2_A-to-I_RNA_Editing_Sites mE_mRNA_L3_12hr_A-to-I_RNA_Editing_Sites mE_mRNA_L3_PS1-2_A-to-I_RNA_Editing_Sites mE_mRNA_L3_PS3-6_A-to-I_RNA_Editing_Sites mE_mRNA_L3_PS7-9_A-to-I_RNA_Editing_Sites mE_mRNA_WPP_A-to-I_RNA_Editing_Sites mE_mRNA_P5_A-to-I_RNA_Editing_Sites mE_mRNA_P6_A-to-I_RNA_Editing_Sites mE_mRNA_P8_A-to-I_RNA_Editing_Sites mE_mRNA_P9-10_A-to-I_RNA_Editing_Sites mE_mRNA_P15_A-to-I_RNA_Editing_Sites mE_mRNA_AdF_Ecl_1days_A-to-I_RNA_Editing_Sites mE_mRNA_AdF_Ecl_5days_A-to-I_RNA_Editing_Sites mE_mRNA_AdF_Ecl_30days_A-to-I_RNA_Editing_Sites mE_mRNA_AdM_Ecl_1days_A-to-I_RNA_Editing_Sites mE_mRNA_AdM_Ecl_5days_A-to-I_RNA_Editing_Sites mE_mRNA_AdM_Ecl_30days_A-to-I_RNA_Editing_Sites
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	For details of animal staging, collection and RNA isolation, see modENCODE_mRNA-Seq_U. (Graveley et al., 2011)
Collection preparation	For details of RNA fragmentation, cDNA synthesis, cDNA cloning and whole genome amplification, see modENCODE_mRNA-Seq_U. (Graveley et al., 2011)
Mode of assay	cDNA was characterized by high-throughput sequencing. See modENCODE_mRNA-Seq_U for details. (Graveley et al., 2011)
Assay platform	Illumina Genome Analyzer II (Graveley et al., 2011)
Data analysis	See modENCODE_mRNA-Seq_U for details of sequencing and read alignments. (Graveley et al., 2011) To identify potential sites of RNA editing, short poly(A)+ RNA-Seq reads that mapped to annotated transcripts were compared to the reference genome to find instances in which a 'G' aligned to an 'A' (for plus strand transcripts) or a 'C' aligned to a 'T' (for minus strand). The first or last six bases of reads were not examined because they were easily mismapped to introns rather than across splice junctions. Only positions with at least five reads showing a substitution from any single developmental stage were considered further. A dataset of potential editing sites with the number of edited reads and the number of non-edited reads for each sample was created. To prevent a polymorphism in the sequenced strain from being reported as editing, at least 100 reads having an exact match to the genome were necessary for further consideration of a potential editing site. Only those sites with at least 5% of reads in at least two independent adult samples showing evidence of editing are reported. (Graveley et al., 2011)
Additional data
	More information is available under: GEO: GPL9061
Associated files
Additional sites
Comments
	927 A-to-I RNA editing sites are listed in Table S29 of the Supplementary Information. (Graveley et al., 2011) A-to-I RNA editing is catalyzed by the Adar protein. (Graveley et al., 2011) Editing at 972 positions was observed within the transcripts of 597 genes. (Graveley et al., 2011) Expressed sequence tags, long poly(A) RNA-Seq and cDNAs cross-validate nearly one-quarter (214) of the newly discovered A-to-I RNA editing sites. (Graveley et al., 2011) For most A-to-I RNA editing sites, the frequency of editing increases throughout development and does not correlate with overall expression levels. (Graveley et al., 2011) RNA editing typically begins in late pupal stages, although some transcripts seem to be edited in late embryogenesis. (Graveley et al., 2011) Three potential editing-associated sequence motifs were identified by computational analysis. (Graveley et al., 2011)
Synonyms & Secondary IDs
Reported As
Symbol Synonym	A-to-I RNA editing sites (Graveley et al., 2011, Graveley et al., 2011) A-to-I RNA Editing Sites (Graveley et al., 2011) mE_A-to-I_RNA_Editing_Sites
Secondary FlyBase IDs

References ( 3 )
Research paper	Graveley et al., 2011, Nature 471(7339): 473--479 The developmental transcriptome of Drosophila melanogaster. [FBrf0213330]
Supplementary material	Graveley et al., 2011, Nature 471(7339): Supplementary Table 29. Summary of A-to-I RNA Editing Sites Discovered. [FBrf0213715] Graveley et al., 2011, Nature 471(7339): Supplementary Information. [FBrf0213508]