HEK: Zhang17 Track Settings
 
Genome-wide identification and differential analysis of translational initiation. (Zhang et al. 2017)   (All Initiating Ribosomes (P-site) tracks)

Display mode:       Reset to defaults

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  
     HEK293 Harr  Ribosome profiles from initiating ribosomes (SRR6327777) (Zhang et al. 2017)   Schema 

Description

Description fromGSE94460: Ribosome protected fragments were extracted from HEK293 cells treated with cycloheximide or harringtonine plus cycloheximide.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP098797). Data from the following samples were processed:

HEK293_Harr Ribosome profiles from initiating ribosomes Homo sapiens(Zhang, et al. 2017)

Adapter sequence AGATCGGAAGAGCACAC and CAGATCGGAAGAGCACA 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 reads below 25 nt were discarded. An offset of 12 nucleotides was then used to get the corresponding P-site of each read.These tracks contain the uniquely mapping reads.,

References

Zhang P, He D, Xu Y, Hou J, Pan BF, Wang Y, Liu T, Davis CM, Ehli EA, Tan L, Zhou F, Hu J, Yu Y, Chen X, Nguyen TM, Rosen JM, Hawke DH, Ji Z, Chen Y (2017) Genome-wide identification and differential analysis of translational initiation. .Nat Commun. 2017 Nov 23;8(1):1749. doi: 10.1038/s41467-017-01981-8.