HEK: Iwasaki 2016 Track Settings
 
Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. (Iwasaki et al. 2016)   (All mRNA-seq Reads tracks)

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     DMSO  mRNA Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     RocA 0  mRNA Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     RocA 3 uM  mRNA Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 

Description

Ribosome profiling, mRNA-Seq, RIP-Seq, and Bind-n-SeqRibosome profiling for sample 1-5, and 11-15. Sample1 and 2 are replicates of control of DMSO treatment for sample 3-5, and 11, with RocA and PP242 treatments. Sample 12 and 13 are replicates of control of DMSO treatment for sample 14 and 15 with Hipp treatments.mRNA-Seq for sample 6-10. Sample 6 and 7 are replicates of control of DMSO treatment for sample 8-10 with RocA treatments.RIP-Seq for 16-19. Sample 16 and 17 are replicates of control of DMSO treatment for sample 18-19 with RocA treatments.Bind-n-Seq for 20-23. Sample 21 is control of DMSO treatment for sample 22-23 with RocA treatments. Sample 20 is a input contol for protein-bound fraction of sample 21.We stably expressed SBP (streptavidin binding peptide)-tagged eIF4A in HEK 293T-REx cells and purified it via M270 streptavidin beads (life techonologies).

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP059825). Data from the following samples were processed:

RocA_3_uM mRNA-seq unique mappers from Homo sapiens(Iwasaki, et al. 2016)
RocA_0 mRNA-seq unique mappers from Homo sapiens(Iwasaki, et al. 2016)
HEK_293_T-REx_cell mRNA-seq unique mappers from Homo sapiens(Iwasaki, et al. 2016)
DMSO mRNA-seq unique mappers from Homo sapiens(Iwasaki, et al. 2016)
RocA_0 mRNA-seq unique mappers from Homo sapiens(Iwasaki, et al. 2016)

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

Iwasaki S, Floor SN, Ingolia NT (2016) Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. . Nature. 2016 Jun 15;534(7608):558-61. doi: 10.1038/nature17978. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't