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General Information
Name
NIH_mRNA_Dpse_2_adults
Species
D. pseudoobscura pseudoobscura
Project type
FlyBase ID
FBlc0000458
Parent Project
    Data Provider
    Title
    Transcriptomes of D. pseudoobscura adult male and female, RNA-Seq.
    Overview
    Description

    Umbrella record for 2 collections of RNA-Seq data from adults. Transcriptome represented as frequency of reads along genome (see GBrowse presentation; data in wiggle format).

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

    Flies were raised in incubators with no photoperiod at 22 C and 60% humidity. Adults were aged 5-7 days post-eclosion and sorted by sex.

    Protocol

    mRNA was purified from total RNA using a QIAGEN Oligotex mRNA kit (Valencia, California). mRNA quality and quantity was determined by Bioanalyzer (Agilent, Santa Clara, California) and 260/280 ratio from Nanodrop ND-1000 UV spectrophotometer. Double-stranded cDNAs were made from mRNA using the Superscript II (Invitrogen) and random hexamer primers (Invitrogen). DNA fragment libraries were prepared for sequencing by addition adaptor oligonucleotides; cDNA templates were size-selected by gel purification (300bp +/- 25bp), then amplified by PCR using oligo-specific primers and Phusion polymerase. The amplified product was purified using a QIAquick column.

    Mode of Assay
    Data analysis

    Only Illumina GAII data was used. Raw reads were trimmed to 75 nt before mapping (shorter reads were removed) and mapped using TopHat (v2.0.8b) with parameters: -g 1 -r 150 --solexa1.3-quals (except for data from head samples where parameters were -g 1 -r 150).

    Comments
    Files
    Additional Information

    [Transcriptional Profiling of additional Drosophila species](http://intermine.modencode.org/release-33/experiment.do?experiment=Transcriptional+Profiling+of+additional+Drosophila+species+with+RNA-Seq)

    Synonyms and Secondary IDs (3)
    Reported As
    Symbol Synonym
    NIH_mRNA_Dpse_2_adults
    Name Synonyms
    Transcriptomes of D. pseudoobscura adult male and female, RNA-Seq.
    Secondary FlyBase IDs
      References (3)