HEK293: Iwasaki19 Track Settings
 
The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. (Iwasaki et al. 2019)   (All Elongating Ribosomes (A-site) tracks)

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     ribo aglaiacized DMSO  Ribosome profiles from elongating ribosomes (SRR5937643, SRR5937644) (Iwasaki et al. 2019)   Schema 
     ribo aglaiacized roca  Ribosome profiles from elongating ribosomes (SRR5937645) (Iwasaki et al. 2019)   Schema 
     ribo naive DMSO  Ribosome profiles from elongating ribosomes (SRR5937641, SRR5937640) (Iwasaki et al. 2019)   Schema 
     ribo naive roca  Ribosome profiles from elongating ribosomes (SRR5937642) (Iwasaki et al. 2019)   Schema 

Description

Description fromGSE102720: Ribosome,profiling

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP115648). Data from the following samples were processed:

ribo_aglaiacized_roca Ribosome profiles from elongating ribosomes Homo sapiens(Iwasaki, et al. 2019)
ribo_naive_DMSO Ribosome profiles from elongating ribosomes Homo sapiens(Iwasaki, et al. 2019)
ribo_aglaiacized_DMSO Ribosome profiles from elongating ribosomes Homo sapiens(Iwasaki, et al. 2019)
ribo_naive_roca Ribosome profiles from elongating ribosomes Homo sapiens(Iwasaki, et al. 2019)

Adapter sequences had already been removed from reads. 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 25 nt were discarded. An offset of 15 nucleotides was then used to get the corresponding A-site of each read.These tracks contain the uniquely mapping reads.,

References

Iwasaki S, Iwasaki W, Takahashi M, Sakamoto A, Watanabe C, Shichino Y, Floor SN, Fujiwara K, Mito M, Dodo K, Sodeoka M, Imataka H, Honma T, Fukuzawa K, Ito T, Ingolia NT (2019) The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. .Mol Cell. 2019 Feb 21;73(4):738-748.e9. doi: 10.1016/j.molcel.2018.11.026. Epub 2018 Dec 27.