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General Information
Name
VDRC-SH
Species
D. melanogaster
Reagent type
FlyBase ID
FBlc0003376
Project
Created by
Vector
    Title
    A set of transgenic RNAi constructs for expression of shRNA under UAS control, VDRC third generation.
    Accessions
      Overview
      Description
      A collection of transgenic lines carrying short RNA hairpins (shRNA) cloned into the pWALIUM20 vector for under GAL4-inducible expression. Constructs were integrated into the attP40 genomic landing site. The collection of shRNA is complementary to the DRSC TRiP resource (no overlap).
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      Biosample Source
      Overview
      Strain
      Stage
      Sex
      Tissue isolated
      Other tissues studied
      Cell component
      Cell line
      Key genes
      Methods
      Sample preparation
      Reagent Details
      Methods
      Protocol
      21nt siRNA oligos were designed to target exons common to all isoforms of a gene using the DSIR website tool. Oligos were compared to SNP resequencing data from 10 Drosophila genomes. For each gene, the best siRNA oligo was selected on a combination of highest predicted activity, lowest off-target probability and absence of common SNPs in a critical position. Any shRNAs exactly matching those at the DRSC TRiP resource were eliminated. Each of the siRNA oligos was then incorporated into a 71nt oligo to generate shRNA (short RNA hairpin). This was cloned pWALIUM20 vector to enable GAL4-inducible expression in germline and somatic cells. Constructs were integrated into the attP40 genomic landing site on the left arm of the second chromosome at 25C6, which has been shown to provide high levels of induced expression of transgenes, yet maintain a low basal expression when the transgenes are not induced.
      21nt siRNA oligos were designed to target exons common to all isoforms of a gene using the DSIR website tool. Oligos were compared to SNP resequencing data from 10 Drosophila genomes. For each gene, the best siRNA oligo was selected on a combination of highest predicted activity, lowest off-target probability and absence of common SNPs in a critical position. Any shRNAs exactly matching those at the DRSC TRiP resource were eliminated. Each of the siRNA oligos was then incorporated into a 71bp oligonucleotide to generate shRNA (short RNA hairpin) as follows. A top strand oligo was designed by concatenating "ctagcagt", the sense-strand oligo (21 nucleotides), "tagttatattcaagcata", the anti-sense oligo, and "gcg". A bottom strand oligo was designed by concatenating "aattcgc", the sense-strand oligo,"tatgcttgaatataacta", the anti-sense oligo, and "actg". This 71bp oligonucleotide was cloned pWALIUM20 vector to enable GAL4-inducible expression in germline and somatic cells. Constructs were integrated into the attP40 genomic landing site on the left arm of the second chromosome at 25C6, which has been shown to provide high levels of induced expression of transgenes, yet maintain a low basal expression when the transgenes are not induced.
      Mode of Assay
      Data analysis
      Comments
      Associated Data
      Size
      Associated features
      725 RNAi_reagent(s)
      Files
      Additional Information
      [More information available at VDRC](http://stockcenter.vdrc.at/control/library_rnai)
      [More information available at VDRC](http://stockcenter.vdrc.at/control/library_vt)
      Synonyms and Secondary IDs (3)
      Reported As
      Symbol Synonym
      VDRC-SH
      shRNA Library
      Name Synonyms
      A set of transgenic RNAi constructs for expression of shRNA under UAS control, VDRC third generation.
      Secondary FlyBase IDs
        References (3)