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General Information
Name
FlyAtlas-RNA.larva
Species
D. melanogaster
Project type
FlyBase ID
FBlc0000175
Parent Project
    Data Provider
    Title
    FlyAtlas transcriptomes of various D. melanogaster larval tissues, microarray.
    Accessions
    Overview
    Description

    Umbrella record for 8 collections that consist of expression microarray data from different tissues of early (feeding) third instar larvae.

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

    Canton-S feeding third instar larvae were reared at 22oC on a 12:12hr light:dark regime on standard Drosophila diet. Tissues were isolated by hand dissection from equal numbers of male and female flies (except in the case of gonads). Multiple samples were pooled to obtain enough total RNA.

    Protocol

    Total RNA was extracted by RNEasy Micro kit (Invitrogen). 2ug of total RNA was used for labeled cRNA synthesis, according to Affymetrix protocol.

    Mode of Assay

    Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45[o]C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the GeneChip scanner 3000 7G.

    Data analysis

    The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. For each tissue, the entire procedure was repeated 4 times, to create 4 independent replicates.

    Comments

    Quantitation of expression at gene level: FlyAtlas provided mean coverage levels for Affy2 probe sets, and FlyBase intersected these probe sets with the exons of all FlyBase genes to associate each probe set with one or more FlyBase genes. These values were distributed into five expression level bins for further analysis.

    Files
    Additional Information
    Synonyms and Secondary IDs (2)
    Reported As
    Symbol Synonym
    FlyAtlas-RNA.larva
    Name Synonyms
    FlyAtlas transcriptomes of various D. melanogaster larval tissues, microarray.
    Secondary FlyBase IDs
      References (3)