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General Information
Name
TSS_mE_CAGE_E16-18hr
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000745
Project
Data Provider
[modENCODE: Drosophila transcriptome](http://www.modencode.org/celniker/)
Title
CAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (16-18 hr AEL), modENCODE.
Status
Current
Accessions
    Biosample Source
    Overview
    Sex
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    Sample preparation

    Adult fly population cages were maintained at 24 ̊C on a 24-hour light cycle (14 hours light/10 hours dark). After a 2hr pre-lay, embryos were collected on agar plates for a 2 hour interval during a light cycle, aged appropriately, dechorionated and frozen on dry ice.

    Biosamples analyzed by this result (1)
    Biosample
    Type
    Title
    D. melanogaster, iso-1 strain, embryo (16-18hr AEL), source for RNA.
    Data Analyzed
    Key genes
    Protocol

    Total RNA was primed for first strand cDNA synthesis using a random N15 primer in the presence of trehalose and sorbitol. The RNA/cDNA hybrid was purified, then capped RNA was biotinylated and purified using streptavidin beads. The first strand cDNA was ligated to another primer at the 5' end for second strand cDNA synthesis. The resulting double-stranded cDNA was cleaved using EcoP15I and a second linker was ligated to the 3' end of the ds-cDNA products. 5'-CAGE tags were purified by streptavidin then amplified by PCR.

    Mode of Assay

    Library was sequenced using Illumina platform.

    Read length (bases):36 (27nt after 9nt adapter trimmed)

    Raw Data Analyzed (1)
    Assay / Reagent collection
    Type
    Title
    CAGE-Seq of D. melanogaster, iso-1 strain, embryo (16-18hr AEL), modENCODE.
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Reference Genome
    Reference Annotation
    Data analysis

    The 9-nt barcode linker sequence was removed, and the 27-nt CAGE reads representing capped 5’ transcript ends were aligned to the D. melanogaster genome using StatMap (http://www.statmap-bio.org/).

    Comments
    Associated Data
    Size
    Files
    Additional Information
    Synonyms and Secondary IDs (3)
    Reported As
    Symbol Synonym
    CAGE em16-18hr
    TSS_mE_CAGE_E16-18hr
    Name Synonyms
    CAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (16-18 hr AEL), modENCODE.
    Secondary FlyBase IDs
      References (1)