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General Information
Name
NIH-Dpse_1_adult_heads
Species
D. pseudoobscura pseudoobscura
Project type
FlyBase ID
FBlc0000445
Parent Project
    Data Provider
    Title
    Transcriptomes of D. pseudoobscura adult male and female head, RNA-Seq.
    Overview
    Description

    Umbrella record for two collections (male and female) of short sequencing reads of cDNA prepared from polyadenylated RNA isolated from heads of Drosophila pseudoobscura adults. Transcriptome represented as frequency of reads along genome (see GBrowse presentation; data in wiggle format); restricted to uniquely aligned reads.

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

    Adults were aged 8 days post-eclosion and sorted by sex. Collection of adult heads: frozen whole flies were placed on 10.8 x 10.8 cm ceramic plates frozen on dry ice; forceps were used to dissect 400-500 heads for subsequent RNA extraction.

    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 (200bp +/- 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

    Strain used: line MV2-25 Baylor sequencing strain, obtained from the Drosophila Species Stock Center (DSSC).

    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-Dpse_1_adult_heads
    Name Synonyms
    Transcriptomes of D. pseudoobscura adult male and female head, RNA-Seq.
    Secondary FlyBase IDs
      References (3)