Open Close
General Information
Name
TSS_RAMPAGE
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000537
Project
Data Provider
Title
Transcription start site regions identified from RAMPAGE RNA-seq profiles.
Status
Current
Accessions
    Biosample Source
    Overview
    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 (36)
    Biosample
    Type
    Title
    D. melanogaster, iso-1 strain, embryo (0-1 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (1-2 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (2-3 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (3-4 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (4-5 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (5-6 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (6-7 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (7-8 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (8-9 hr AEL), source for RNA.
    D. melanogaster, iso-1 strain, embryo (9-10 hr AEL), source for RNA.
    Showing 10 / 36 records. Use Export to HitList above to see all
    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.
    Read length (bases): 76
    Total reads: 296,251,429
    Uniquely mapped reads: 228,277,829
    Raw Data Analyzed (36)
    Assay / Reagent collection
    Type
    Title
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, adult male (5d post-eclosion).
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, embryo (1-2 hr AEL).
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, embryo (2-3 hr AEL).
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, embryo (12-13 hr AEL).
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, embryo (14-15 hr AEL).
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, embryo (16-17 hr AEL).
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, embryo (20-21 hr AEL).
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, embryo (21-22 hr AEL).
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, second instar larva.
    RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, late third instar larva (clear gut).
    Showing 10 / 36 records. Use Export to HitList above to see all
    Processed Data Analyzed (36)
    Result
    Type
    Title
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, adult female (5d post-eclosion).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, adult male (5d post-eclosion).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (0-1 hr AEL).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (1-2 hr AEL).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (10-11 hr AEL).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (11-12 hr AEL).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (12-13 hr AEL).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (13-14 hr AEL).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (14-15 hr AEL).
    RAMPAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (15-16 hr AEL).
    Showing 10 / 36 records. Use Export to HitList above to see all
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Dmel R5.32
    Data analysis
    For peak calling, PCR duplicates, defined as reads sharing the same alignment, were removed from individual data sets. Data for the 36 different stages were combined for peak calling. To account for non-specific signal from abundant transcripts, 5' end frequency was normalized to transcript abundance as measured by the 3' portion of the paired end reads. Peaks were called by a sliding window algorithm that assesses the significance of local signal enrichment given a null distribution. Signal-enriched windows in close proximity to each other are merged into peaks, and those were subsequently trimmed at the edges down to the first base with signal.
    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
    Associated features
    31,078 transcription_start_site(s)
    Files
    Additional Information
    Synonyms and Secondary IDs (4)
    Reported As
    Symbol Synonym
    RAMPAGE TSS
    TSS_RAMPAGE
    Transcription_Start_Sites_RAMPAGE
    Name Synonyms
    Transcription start site regions identified from RAMPAGE RNA-seq profiles.
    Secondary FlyBase IDs
      References (3)