KOPT-K1: Wolfe 2014 Track Settings
 
RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. (Wolfe et al. 2014)   (All Elongating Ribosomes (A-site) tracks)

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     DMSO treated RF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Wolfe et al. 2014)   Schema 
     Silvestrol 25 nM treated RF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Wolfe et al. 2014)   Schema 

Description

Comparison of ribosome-protected RNA for drug treated and DMSO treated KOPT-K1 cell, two replicates of ribosome-protected RNA sequencing and three replicates of RNA-seq.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP041255). Data from the following samples were processed:

Silvestrol_25_nM_treated_RF Ribosome profiling data from Homo sapiens(Wolfe, et al. 2014)
DMSO_treated_RF Ribosome profiling data from Homo sapiens(Wolfe, et al. 2014)

Adapter sequence CTGTAGGCACCATCAAT was removed from reads using Cutadapt An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. An alignment to the hg38 genome assembly was performed using Bowtie, and reads below 25nt were discarded. These tracks contains the uniquely mapping reads.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.

References

Wolfe AL, Singh K, Zhong Y, Drewe P, Rajasekhar VK, Sanghvi VR, Mavrakis KJ, Jiang M, Roderick JE, Van der Meulen J, Schatz JH, Rodrigo CM, Zhao C, Rondou P, de Stanchina E, Teruya-Feldstein J, Kelliher MA, Speleman F, Porco JA Jr, Pelletier J, Ratsch G, Wendel HG (2014) RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. . Nature. 2014 Sep 4;513(7516):65-70. doi: 10.1038/nature13485. Epub 2014 Jul 27. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't