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General Information
Name
mE_mRNA_AdF_Ecl_1days_EXTRA_junctions
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000485
Title
Additional (low confidence) RNA-Seq exon junctions in D. melanogaster, iso-1 strain, adult female (1 day post-eclosion), modENCODE.
Status
Current
Accessions
    Biosample Source
    Overview
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    Sample preparation

    Fly stocks were reared in bottles at 24oC and females were collected immediately after eclosion, then frozen on dry ice.

    Biosamples analyzed by this result (1)
    Biosample
    Type
    Title
    D. melanogaster, iso-1 strain, adult female (1 day post-eclosion), source for RNA.
    Data Analyzed
    Key genes
    Protocol

    Frozen samples were homogenized and extracted using the TRIzol reagent protocol (Invitrogen). RNA was purified on an RNeasy spin column (Qiagen), and DNase treated. Polyadenylated RNAs were purified from total RNA extracts via oligo(dT) binding, using standard Illumina protocol. The poly(A)+ RNA was fragmented using divalent cations under elevated temperature, following by first and second strand cDNA synthesis primed with random hexamers. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase, and phosphorylated at their 5' ends with T4 polynucleotide kinase. After adding A bases to the 3' end of the DNA fragments, Illumina adaptor oligonucleotides were ligated to the ends and ~ 300 bp fragments were isolated from an agarose gel, enriched by PCR amplification, and gel-purified again.

    Mode of Assay

    Read length (bases):76

    The samples were quantitated using a Nanodrop, and loaded onto a flow cell for cluster generation and sequenced on an Illumina Genome Analyzer II using either single read or paired end protocols (Illumina).

    Raw Data Analyzed (1)
    Assay / Reagent collection
    Type
    Title
    RNA-Seq of D. melanogaster, iso-1 strain, adult female (1 day post-eclosion), modENCODE, unstranded.
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Data analysis

    These junctions were excluded from the original exon junction identification analysis because they supported gene merges and were not cross validated by another data source. The full list has been provided to FlyBase, and only those junctions that come to be supported by additional evidence are made public.

    Comments
    Associated Data
    Size
    Files
    Additional Information
    Synonyms and Secondary IDs (4)
    Reported As
    Symbol Synonym
    adult_female_1d
    mE_mRNA_AdF_Ecl_1days_EXTRA_junctions
    Name Synonyms
    Additional (low confidence) RNA-Seq exon junctions in D. melanogaster, iso-1 strain, adult female (1 day post-eclosion), modENCODE.
    Secondary FlyBase IDs
      References (1)