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

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     DMSO  Ribosome Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     HEK 293 T-REx cell  Ribosome Profiles of elongating ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     Hipp 0  Ribosome Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     Hipp 1 uM  Ribosome Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     PP242 2  Ribosome Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     RocA 0  Ribosome Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     RocA 3 uM  Ribosome Coverage of ribosomes from Homo sapiens (Iwasaki et al. 2016)   Schema 
     Roca_0.3  Ribosome Profiles of elongating 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 Ribosome coverage data from Homo sapiens(Iwasaki, et al. 2016)
RocA_0 Ribosome coverage data from Homo sapiens(Iwasaki, et al. 2016)
Hipp_1_uM Ribosome coverage data from Homo sapiens(Iwasaki, et al. 2016)
Hipp_0 Ribosome coverage data from Homo sapiens(Iwasaki, et al. 2016)
PP242_2 Ribosome coverage data from Homo sapiens(Iwasaki, et al. 2016)
DMSO Ribosome coverage data from Homo sapiens(Iwasaki, et al. 2016)
HEK_293_T-REx_cell Ribosome coverage data from Homo sapiens(Iwasaki, et al. 2016)
RocA_0 Ribosome coverage data 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