CG5422 (Rox8), Unique mapper

RNAi CG5422 in S2-DRSC RNA-seq uniquely mapping reads (Celniker project, Graveley subgroup)

Details

RNA-seq analysis was performed on biological replicates of poly(A)+ RNA extracted from D. melanogaster S2-DRSC cells treated with dsRNA targeting Rox8 (CG5422). Uniquely aligned reads were mapped using Bowtie. Tracks show alignments and read density.

General Description

The goal of these experiments are to identify splicing events that are regulated by specific RNA binding proteins in Drosophila S2 cells. From this collection of regulated exons, we will attempt to identify motifs that are enriched in and/or around the regulated exons and are therefore the best candidates for being recognized by the RNA binding protein. To do this, we are using RNAi to deplete individual RNA binding protein mRNAs from Drosophila S2-DRSC cells and then using RNA-Seq to characterize the resulting transcriptome. Comparison of the transcriptome from depleted cells to that of un-depleted cells will allow us to identify regulated splicing events.

Protocols

  1. Growth and isolation: S2-DRSC cell line growth, mRNA purification from total RNA, Paired-end sample prep
  2. Other Protocols: RNAi in cell culture, Graveley single_end sequencing, Bowtie alignment for single-end reads


Release Date: 2011-04-23