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General Information
Name
TSS_RAMPAGE_E14-15hr
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000552
Project
Data Provider
Title
RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (14-15 hr AEL).
Status
Current
Accessions
    Biosample Source
    Overview
    Sex
    Tissue isolated
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    Sample preparation

    Embryos were collected in one-hour windows on grape-agar plates after two two-hour prelays and aged appropriately. Embryos were dechorionated and snap frozen in liquid nitrogen.

    Biosamples analyzed by this result (1)
    Biosample
    Type
    Title
    D. melanogaster, iso-1 strain, embryo (14-15 hr AEL), source for RNA.
    Data Analyzed
    Key genes
    Protocol

    Total RNA was isolated using the RNAdvance Tissue kit (Agencourt) and treated with DNase I. RNA quality was checked on a Bioanalyzer (Agilent). 5'-monophosphate RNA species, mainly ribosomal RNA, were depleted by TEX digest (Epicentre). Reverse transcriptase was done under conditions that promote "template switching" to preferentially add linkers to the 5' ends of 5'-complete cDNAs for second strand synthesis. 5'-capped RNA molecules were then biotinylated and pulled down to serve as templates for second strand cDNA synthesis. cDNA was PCR amplified and DNA quality was confirmed on a DNA HS Bioanalyzer chip.

    Three multiplexed libraries were prepared: one for embryos (24 samples), one for larvae and pupae (10 samples) and one for adults (two samples).

    Mode of Assay

    Read length (bases): 101

    Samples were processed as multiplexed libraries: one that pooled all 24 embryonic samples, one that pooled all 10 larval and pupal samples, and one that pooled both adult fly samples.

    Total reads: 3,732,348

    Read length (bases): 76

    Uniquely mapped reads: 2,922,415

    Total reads: 296,251,429

    Uniquely mapped reads: 228,277,829

    Raw Data Analyzed (1)
    Assay / Reagent collection
    Type
    Title
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, embryo (14-15 hr AEL).
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Reference Genome
    Reference Annotation
    Data analysis

    Sequences corresponding to library identification barcodes and primers were trimmed. Reads were mapped with STAR. All uniquely mapping reads were kept. For multiply mapping reads, if all alignments started within an annotated transposon and overlapped the same gene annotation, the alignment starting in the closest transposon was selected. Transcript annotations were obtained from FlyBase (release 5.32).

    Comments
    Associated Data
    Size
    2,922,415 uniquely mapped reads
    Files
    Additional Information
    Synonyms and Secondary IDs (4)
    Reported As
    Symbol Synonym
    TSS_RAMPAGE_E14-15hr
    Transcription_Start_Sites_RAMPAGE_em14-15hr
    Name Synonyms
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (14-15 hr AEL).
    Secondary FlyBase IDs
      References (1)