HEK: Sidrauski 2015 Track Settings
 
The Small Molecule ISRIB Reverses the Effects of eIF2α Phosphorylation on Translation and Stress Granule Assembly (Sidrauski et al. 2015)   (All Elongating Ribosomes (Footprints) tracks)

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     ribo isrib  Ribosome Coverage of elongating ribosomes from Homo sapiens (Sidrauski et al. 2015)   Schema 
     ribo tm  Ribosome Coverage of elongating ribosomes from Homo sapiens (Sidrauski et al. 2015)   Schema 
     ribo tmisrib  Ribosome Coverage of elongating ribosomes from Homo sapiens (Sidrauski et al. 2015)   Schema 
     ribo untr  Ribosome Coverage of elongating ribosomes from Homo sapiens (Sidrauski et al. 2015)   Schema 

Description

Ribosome profiling with paired RNA-seq.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP053402). Data from the following samples were processed:

ribo_untr Ribosome coverage data from Homo sapiens(Sidrauski, et al. 2015)
ribo_tm Ribosome coverage data from Homo sapiens(Sidrauski, et al. 2015)
ribo_tmisrib Ribosome coverage data from Homo sapiens(Sidrauski, et al. 2015)
ribo_isrib Ribosome coverage data from Homo sapiens(Sidrauski, et al. 2015)

Adapter sequence CTGTAGGCACCATCAATAGATCGGA was removed from reads using CutadaptAn 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

Sidrauski C, McGeachy AM, Ingolia NT, Walter P (2015) The Small Molecule ISRIB Reverses the Effects of eIF2α Phosphorylation on Translation and Stress Granule Assembly . Elife. 2015 Feb 26;4. doi: 10.7554/eLife.05033. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't