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General Information
Name
RNA-Seq_mE_L_Sindbis_virus
Species
D. melanogaster
Assay type
FlyBase ID
FBlc0001466
Project
Data Provider
Title
RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, larva, Sindbis virus treatment.
Accessions
Biosample Source
Overview
Sex
Tissue isolated
Other tissues studied
Cell component
Cell line
Key genes
Sample preparation

A transgenic stock carrying the constructs P{Act5C-GAL4} and P{UAS-SINrep.GFP} on the same chromosome was used to constitutively express non-structural components of the Sindbis virus (see FBrf0208818). This stock was crossed to Oregon R virgin females, and males expressing the GFP-tagged Sindbis proteins were selected for breeding. This procedure was continued for 10 further generations to place the transgenes into the same genetic background as other treatment experiments. Larvae (mixed stage and sex) were collected after the 12th generation and flash frozen in liquid nitrogen for RNA preparation.

Biosamples used (1)
Biosample
Type
Title
D. melanogaster, Oregon-R-modENCODE strain, larva, Sindbis virus treatment, source for RNA.
Assay Details
Key genes
Protocol

For the Sindbis virus, resveratrol and rotenone/starved treatment samples, the RNA-Seq libraries were generated using a dUTP-based method (PMID: 22955620) that gives 90% to 97% stranded data. The Illumina kit used for the other treatment samples give 99% stranded data.

Total RNA was isolated using Trizol, then Qiagen RNeasy spin columns. mRNA was isolated using Dynal oligo(dT) beads, then fragmented using divalent cations under elevated temperature, followed by sequential ligation of RNA linkers to the 5’ and 3’ ends. Next, reverse transcription was performed using a primer complementary to the 3’ linker and PCR was performed using primers complementary to both linkers. ~ 300 bp fragments were isolated from an agarose gel and gel-purified again.

Mode of Assay

Read length (bases):101

The samples were quantitated using a Nanodrop, and loaded onto a flow cell for cluster generation and sequenced on an Illumina Genome Analyzer II using either single read or paired end protocols (Illumina).

Comments
Associated Data
Size
Files
Additional Information
Synonyms and Secondary IDs (2)
Reported As
Symbol Synonym
RNA-Seq_mE_L_Sindbis_virus
Name Synonyms
RNA-Seq of D. melanogaster, Oregon-R-modENCODE strain, larva, Sindbis virus treatment.
Secondary FlyBase IDs
    References (2)