GSE35585
GSE35585: RIP-seq from ENCODE/SUNY Albany
Summary:     The RNA binding protein (RBP) associated mRNA sequencing track (RIP-Seq) is produced as part of the Encyclopedia of DNA Elements (ENCODE) Project (http://hgwdev.cse.ucsc.edu/ENCODE/index.html). This track displays transcriptional fragments associated with RBP in cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType) K562 and GM12878, using Ribonomic profiling via Illumina SBS.  In eukaryotic organisms gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Seq profiling.    For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf  Overall Design: RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). RNA samples were amplified and converted to cDNA with the Nugen (http://www.nugeninc.com/) Ovation© RNA-Seq System and prepped for sequencing with the Illumina (http://www.illumina.com/) mRNA-Seq protocol. Approximately 30 million single end sequencing reads were obtained for each K562 and GM12878. RIP samples were analyzed for signal that was at or above the 60th percentile and statistically enriched compared to the negative control. Sequences were analyzed using TopHat (http://tophat.cbcb.umd.edu/) (Trapnell et al., 2009) with Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead et al., 2009).Peaks were called from the top 40% of TopHat normalized reads, with a max gap, min run of (24:48). Unions of overlapping peak regions from total RNA replicates (RIP-Input) are presented with p-value from a one tailed t-test for average signal from replicates versus 0 (no cut-off was used for totals). Replicate overlap for positive RIP treatment peaks (ELAVL1 and PABPC1) are presented with a p-value from one tailed t-test versus signal for same the region in negative control replicates (T7-tag). RIP peaks were from sequences longer than 120 bp and p-value < .05. For both totals (RIP-input) and RIPs, the peak scores are scaled relative p-values between treatment and control.