FB2019_05, released Oct 15, 2019

Result: Knoblich_mRNA_L3_CNS_neuron

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General Information
Name
Knoblich_mRNA_L3_CNS_neuron
Species
D. melanogaster
Result type
RNA-seq profile
FlyBase ID
FBlc0000506
Project
Data Provider
Title
RNA-Seq coverage profile for D. melanogaster, larval neuron.
Status
Current
Accessions
    Biosample Source
    Overview
    Strain
    Stage
    larval stage
    (Berger et al., 2012)
    Sex
    Tissue isolated
    embryonic/larval neuron
    (Berger et al., 2012)
    embryonic/larval central nervous system
    (Berger et al., 2012)
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    targeted cell labeling
    (Berger et al., 2012)
    Sample preparation
    Neural cells were fluorescently labeled using GFP under the control of ase regulatory sequences and FACS-sorted into neuroblasts and neurons. Neuroblasts were distinguished by their strong GFP signal, large size and relatively small population, while neurons were identified by their weaker GFP signal, smaller size and greater abundance.
    Biosamples analyzed by this result (1)
    Biosample
    Type
    Title
    BS_Knoblich_L3_CNS_neuron
    isolated cells
    D. melanogaster, larval neuron, source for RNA.
    Data Analyzed
    Assay
    RNA-Seq
    (Berger et al., 2012)
    Assay methods
    paired-end layout
    (Berger et al., 2012)
    poly(A) RNA isolation
    (Berger et al., 2012)
    Illumina sequencing
    (Berger et al., 2012)
    Key genes
    Protocol
    Total RNA was isolated from 28-35 million FACS-sorted neurons using Trizol. Polyadenylated mRNA was enriched for using oligo(dT) beads. The poly(A)+ RNA was fragmented using divalent cations under elevated temperature.
    Poly(A)+ RNA was subjected to first strand cDNA synthesis. Second strand cDNA synthesis was done in the presence of UTP to generate stranded cDNA libraries. Double-stranded cDNA was end-repaired and ligated to adapters. After size selection (200-600bp) and UDG-ase treatment for strand specificity, DNA was PCR amplified and the quality assessed by Agilent bioanalyzer.
    Mode of Assay
    Read length (bases):76
    (Berger et al., 2012)
    Raw Data Analyzed (1)
    Assay / Reagent collection
    Type
    Title
    RNA-Seq_GSE38764_L3_CNS_neuron
    RNA-Seq
    RNA-Seq of D. melanogaster, larval neuron.
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    stranded profile
    (Berger et al., 2012)
    uniquely mapping read alignment
    (Berger et al., 2012)
    Reference Genome
    Reference Annotation
    Data analysis
    Strand-specific paired end reads were filtered for rRNA sequences. Filtered reads were then aligned using TopHat (v1.4.1) against the D. melanogaster genome (FlyBase r5.44) and a maximum of six mismatches. Introns between 20 and 150,000 bp were allowed. snRNA, rRNA, tRNA, snoRNA and pseudogenes were masked.
    Comments
    Associated Data
    Size
    28715786 Number of unique reads.
    (Berger, 2012.10.16)
    Files
    Additional Information
    The RNA-seq profiles displayed by FlyBase in GBrowse and used for RPKM calculation can be accessed at the FTP link below as .wig files. Please take note of how these FlyBase .wig files represent data for a contiguous sequence of bases with the same signal value. The value is declared only for the first position of that region, and applies to all positions that follow (these are not explicitly listed) until a new value at a new base position is declared.
    (FlyBase Curators, 2013)
    Synonyms and Secondary IDs (3)
    Reported As
    Symbol Synonym
    Knoblich_mRNA_L3_CNS_neuron
    (Emmert, 2014.6.4)
    neuron transcriptome
    (Berger et al., 2012)
    Name Synonyms
    RNA-Seq coverage profile for D. melanogaster, larval neuron.
    (Berger et al., 2012)
    Secondary FlyBase IDs
      References (6)