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General Information
Name
Rosbash_Adult_Head_A-to-I_Editing_Sites
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000519
Project
Data Provider
Title
A-I RNA editing sites identified from RNA-Seq of nascent nuclear RNA from adult heads.
Status
Current
Accessions
    Biosample Source
    Overview
    Strain
    Sex
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Sample preparation
    Flies were collected at circadian time ZT10. Whole flies were frozen and adult heads were isolated using brass sieves. Tissue was homogenized on ice, filtered to remove debris, and centrifuged on a sucrose cushion to isolate nuclei.
    Flies were entrained under 12hr:12hr light:dark cycles for 3-4 days.
    Biosamples analyzed by this result (6)
    Biosample
    Type
    Title
    D. melanogaster, yw, adult head, ZT10, source for nuclear RNA.
    D. melanogaster, yw, adult head, ZT14, source for nuclear RNA.
    D. melanogaster, yw, adult head, ZT18, source for nuclear RNA.
    D. melanogaster, yw, adult head, ZT2, source for nuclear RNA.
    D. melanogaster, yw, adult head, ZT22, source for nuclear RNA.
    D. melanogaster, yw, adult head, ZT6, source for nuclear RNA.
    Data Analyzed
    Key genes
    Protocol
    Total RNA was extracted from isolated nuclei using Trizol. Replicate 1 was depleted of ribosomal RNA, replicate 2 was not. For both replicates, mRNA was depleted by two rounds of poly(A) RNA depletion. Sequencing library was constructed per standard Illumina protocol.
    Mode of Assay
    Raw Data Analyzed (6)
    Assay / Reagent collection
    Type
    Title
    RNA-Seq of nascent nuclear RNA from D. melanogaster, yw, adult head, ZT2.
    RNA-Seq of nascent nuclear RNA from D. melanogaster, yw, adult head, ZT6.
    RNA-Seq of nascent nuclear RNA from D. melanogaster, yw, adult head, ZT10.
    RNA-Seq of nascent nuclear RNA from D. melanogaster, yw, adult head, ZT14.
    RNA-Seq of nascent nuclear RNA from D. melanogaster, yw, adult head, ZT18.
    RNA-Seq of nascent nuclear RNA from D. melanogaster, yw, adult head, ZT22.
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Data analysis
    RNA sequences were mapped to the reference genome using TopHat. Potential A-to-I editing sites were only considered if they were observed in at least ten of 12 replicates and no G residues were observed at the same position in parallel DNA-Sequencing of the same strain (39X coverage).
    Comments
    Associated Data
    Size
    Files
    Additional Information
    Synonyms and Secondary IDs (3)
    Reported As
    Symbol Synonym
    Cotranscriptional A-to-I editing
    Rosbash_Adult_Head_A-to-I_Editing_Sites
    Name Synonyms
    A-I RNA editing sites identified from RNA-Seq of nascent nuclear RNA from adult heads.
    Secondary FlyBase IDs
      References (3)