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 (A-site) tracks)

Display mode:       Reset to defaults

Overlay method:
Type of graph:
Track height: pixels (range: 11 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 127)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
List subtracks: only selected/visible    all  
     ribo isrib  Ribosome Profiles of elongating ribosomes from Homo sapiens (Sidrauski et al. 2015)   Schema 
     ribo tm  Ribosome Profiles of elongating ribosomes from Homo sapiens (Sidrauski et al. 2015)   Schema 
     ribo tmisrib  Ribosome Profiles of elongating ribosomes from Homo sapiens (Sidrauski et al. 2015)   Schema 
     ribo untr  Ribosome Profiles 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 profiling data from Homo sapiens(Sidrauski, et al. 2015)
ribo_tm Ribosome profiling data from Homo sapiens(Sidrauski, et al. 2015)
ribo_tmisrib Ribosome profiling data from Homo sapiens(Sidrauski, et al. 2015)
ribo_isrib Ribosome profiling 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.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.

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