MDA-MB-231: Rubio 2014 Track Settings
 
Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. (Rubio et al. 2014)   (All mRNA-seq Reads tracks)

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     mRNA dmso 2hr  mRNA Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     mRNA silvestrol 2hr  mRNA Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     totRNA dmso  mRNA Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     totRNA ink128  mRNA Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 

Description

Translation efficiency (TE) of mRNAs dervied from ribosome footprints was monitored in the presence or absence of 25 nM Silvestrol, an inhibitor of eukaryotic translation initiation factor 4A (eIF4A). Transcripts with reduced TE in the presence of Silvestrol were compare to transcripts with reduced TE in the presence of INK128, a catalytic mTOR inhbitor.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP047065). Data from the following samples were processed:

mRNA_dmso_2hr mRNA-seq unique mappers from Homo sapiens(Rubio, et al. 2014)
totRNA_ink128 mRNA-seq unique mappers from Homo sapiens(Rubio, et al. 2014)
mRNA_silvestrol_2hr mRNA-seq unique mappers from Homo sapiens(Rubio, et al. 2014)
totRNA_dmso mRNA-seq unique mappers from Homo sapiens(Rubio, 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 these tracks contains the uniquely mapping reads.

References

Rubio CA, Weisburd B, Holderfield M, Arias C, Fang E, DeRisi JL, Fanidi A (2014) Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. . Genome Biol. 2014;15(10):476. Research Support, Non-U.S. Gov't