General Information
Name
mE_Transcription_Start_Sites
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000202
Project
Data Provider
Title
Transcription start site regions identified by analysis of embryonic ESTs, RLM-RACE and CAGE-Seq.
Status
Current
Accessions
    Biosample Source
    Overview
    Sex
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    Sample preparation
    For the RE cDNA library, embryos at 0-22 hr AEL were collected from an isogenic y; cn bw sp (iso-1) strain.
    Biosamples analyzed by this result (3)
    Biosample
    Type
    Title
    D. melanogaster, iso-1 strain, embryo, source for RNA.
    D. melanogaster, iso-1 strain, embryo (0-22 hr), source for cDNA.
    D. melanogaster, iso-1 strain, embryo, source for cDNA.
    Data Analyzed
    Key genes
    Protocol
    RNA was polyA+ selected twice (RNA made by L. Hong). cDNA was synthesized by priming with the oligo(dT) primer adapter (5'-GAGAGAGAGAGGATCCAATACTGGAGAGTTTTTTTTTTTTTTTTVN-3'). The first strand was synthesized in presence of trehalose, which increases the full-length cDNA synthesis (Carninci, P. et al. 1998. Proc. Natl. Acad. Sci. U.S.A. 95(2): 520-524; Carninci, P. et al. 1999. Methods Enzymol. 303: 19-44). Full-length cDNA was selected with the biotinylated cap-trapper (Carninci, P. et al. 1996. Genomics 37(3): 327-336). A linker was then ligated to the single-strand cDNA following the published protocol (Shibata, Y., et al. 2001. Biotechniques 30(6): 1250-1254). Subsequently, the cDNA was normalized by using RoT=1.0 as published (Carninci, P., et al. 2000. Genome Res. 10(10): 1617-1630). Second strand cDNA was primed with the (5'-AGAGAGAGAGCTCGAGCTCTAATAAGGTGACACTATAGAACCA-3') primer. After restriction digestion of the hemimethylated cDNA with BamHI and XhoI, the cDNA was cloned in the lambda FLC-I vector. Subsequently, the library was bulk-excised into pFLC-I plasmid as described (Carninci, P., et al. 2001. Genomics 77(1-2): 79-90). cDNAs were transformed into DH5-alpha TonA strain.
    Mode of Assay
    Raw Data Analyzed (3)
    Assay / Reagent collection
    Type
    Title
    CAGE-Seq of D. melanogaster, iso-1 strain, embryo (0-24hr AEL), modENCODE.
    RE cap-trapped cDNA library of D. melanogaster, iso-1 strain, embryo (0-22 hr).
    RNA-Seq of D. melanogaster, iso-1 strain, embryo, 5' ends of capped transcripts.
    Processed Data Analyzed (1)
    Result
    Type
    Title
    CAGE-Seq capped mRNA 5' end profile for D. melanogaster, iso-1 strain, embryo (0-24 hr AEL), modENCODE.
    Analysis
    Methods
    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
    modENCODE Transcription Start Sites
    Core promoter sequence motifs are differentially enriched in the peaked and broad classes of promoters.
    Genes with peaked promoters have a marked and highly significant tendency to be expressed in spatially and temporally restricted patterns, and genes with broad promoters do not.
    CAGE peaks within 3' UTRs appear to be associated with cytoplasmic transcript degradation products, and not independent promoters.
    Associated Data
    Size
    Associated features
    12,454 transcription_start_site(s)
    Files
    Additional Information
    Synonyms and Secondary IDs (4)
    Reported As
    Symbol Synonym
    Integrated promoters
    mE_Transcription_Start_Sites
    modENCODE_TSS
    Name Synonyms
    Transcription start site regions identified by analysis of embryonic ESTs, RLM-RACE and CAGE-Seq.
    Secondary FlyBase IDs
      References (3)