CG6227, Multi mapper

RIP-seq D.mel splicing factor CG6227 TopHat alignment r5 (Celniker project, Graveley subgroup)


Reads were sequenced from Drosophila melanogaster RNA libraries made from S2R+ cells transformed with CG6227, and aligned with TopHat against the r5 genome. Because the samples are IPs of total cell lysates, which most likely include a high fraction of rRNA, and only unique alignments were retained, the alignment rates appear artificially low. Tracks show unique read alignments and density
Total read count: 87987591
Mapped read count: 14555047
Alignment rate: 16%

General Description

The goal of these experiments is to identify RNAs bound by individual RNA-binding proteins. Drosophila S2R+ cells were transiently transfected with vectors encoding the indicated HA-tagged RNA-binding proteins, or without an insert as a control. Expression was induced with CuSO4, whole cell lysates were prepared and protein-RNA complexes were isolated by immunoprecipitation with HA immunoaffinity resin. RNA was then isolated from the immunoprecipitated material, and RNA-Seq libraries were prepared using Illumina Tru-Seq mRNA kits and sequenced on the Illumina GAIIx or HiSeq2000. Sequence reads were aligned to the D. melanogaster reference genome r5 using TopHat and expression levels were quantitated using Cufflinks.


  1. Data Analysis: TopHat for RIP-seq
  1. External Links: GSM927211, GSM927212, SRR494060, SRR494061

Referenced modENCODE submissions:

Release Date: 2012-06-29