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General Information
Name
TSS_MachiBase
Species
D. melanogaster
Project type
FlyBase ID
FBlc0000725
Parent Project
    Data Provider
    [MachiBase](http://machibase.gi.k.u-tokyo.ac.jp/)
    Title
    Profile of mRNA transcript 5'-ends for various developmental stages, CAGE-Seq, MachiBase.
    Accessions
    Overview
    Description

    Genomic sequences identified as transcription start sites (TSS); the 5' ends of cDNAs were identified using 5'-end SAGE.

    Reagent type
    Key genes
    GO term(s)
    SO term(s)
    Details
    Sample preparation
    Protocol

    5'-ends of capped transcripts were isolated by 5'-SAGE. Briefly, a biotinylated adapter to 5'-phosphate ends exposed after cleavage of the 5'-cap by tobacco acid pyrophosphatase (TAP). Double-stranded cDNAs were then cleaved with MmeI to generate short 25-27nt fragments, and biotinylated adapters (along with adjacent 5'end sequence) are purified. These SAGE fragments were then used for Illumina library construction (single end layout).

    Mode of Assay

    Total reads: 51,764,976

    Uniquely aligned reads: 25,083,481

    Read length (bases): 25-27

    Data analysis

    Reads were mapped to Dmel genome annotation R5.3 using a parallel version of BLAT. Only uniquely mapped reads were considered (allowing for up to 3 mismatches). Associated TSS profiles represent mapped 5'-ends.

    Comments
    Files
    Additional Information
    Synonyms and Secondary IDs (3)
    Reported As
    Symbol Synonym
    MachiBase TSSs
    TSS_MachiBase
    Name Synonyms
    Profile of mRNA transcript 5'-ends for various developmental stages, CAGE-Seq, MachiBase.
    Secondary FlyBase IDs
      References (1)