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

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     FP dmso  Ribosome Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP dmso 1hr  Ribosome Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP dmso 2hr  Ribosome Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP dmso 2hr br  Ribosome Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP ink128  Ribosome Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP silvestrol 1hr  Ribosome Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP silvestrol 2hr  Ribosome Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP silvestrol 2hr br  Ribosome Coverage of ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP untreated  Ribosome 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:

FP_silvestrol_1hr Ribosome coverage data from Homo sapiens(Rubio, et al. 2014)
FP_ink128 Ribosome coverage data from Homo sapiens(Rubio, et al. 2014)
FP_silvestrol_2hr_br Ribosome coverage data from Homo sapiens(Rubio, et al. 2014)
FP_silvestrol_2hr Ribosome coverage data from Homo sapiens(Rubio, et al. 2014)
FP_untreated Ribosome coverage data from Homo sapiens(Rubio, et al. 2014)
FP_dmso_1hr Ribosome coverage data from Homo sapiens(Rubio, et al. 2014)
FP_dmso_2hr_br Ribosome coverage data from Homo sapiens(Rubio, et al. 2014)
FP_dmso Ribosome coverage data from Homo sapiens(Rubio, et al. 2014)
FP_dmso_2hr Ribosome coverage data 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