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 (A-site) tracks)

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     FP dmso  Ribosome Profiles of elongating ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP dmso 1hr  Ribosome Profiles of elongating ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP dmso 2hr  Ribosome Profiles of elongating ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP dmso 2hr br  Ribosome Profiles of elongating ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP ink128  Ribosome Profiles of elongating ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP silvestrol 1hr  Ribosome Profiles of elongating ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP silvestrol 2hr  Ribosome Profiles of elongating ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP silvestrol 2hr br  Ribosome Profiles of elongating ribosomes from Homo sapiens (Rubio et al. 2014)   Schema 
     FP untreated  Ribosome Profiles of elongating 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 profiling data from Homo sapiens(Rubio, et al. 2014)
FP_ink128 Ribosome profiling data from Homo sapiens(Rubio, et al. 2014)
FP_silvestrol_2hr_br Ribosome profiling data from Homo sapiens(Rubio, et al. 2014)
FP_silvestrol_2hr Ribosome profiling data from Homo sapiens(Rubio, et al. 2014)
FP_untreated Ribosome profiling data from Homo sapiens(Rubio, et al. 2014)
FP_dmso_1hr Ribosome profiling data from Homo sapiens(Rubio, et al. 2014)
FP_dmso_2hr_br Ribosome profiling data from Homo sapiens(Rubio, et al. 2014)
FP_dmso Ribosome profiling data from Homo sapiens(Rubio, et al. 2014)
FP_dmso_2hr Ribosome profiling 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.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.

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