HCT116:Crappe 2015 Track Settings
 
PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration. (Crappe et al. 2015)   (All Elongating Ribosomes (A-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  
     Cycloheximide treated HCT116  Ribosome Profiles of elongating ribosomes from Homo sapiens (Crappe et al. 2015)   Schema 

Description

Ribosome profiling of lactimidomycin and cycloheximide treated HCT116 cells

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP042937). Data from the following samples were processed:

Cycloheximide_treated_HCT116 Ribosome profiling data from Homo sapiens(Crappe, et al. 2015)

Adapter sequence AGATCGGAAGAGCACAC 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 25nt were discarded. 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

Crappe J, Ndah E, Koch A, Steyaert S, Gawron D, De Keulenaer S, De Meester E, De Meyer T, Van Criekinge W, Van Damme P, Menschaert G (2015) PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration. . Nucleic Acids Res. 2015 Mar 11;43(5):e29. doi: 10.1093/nar/gku1283. Epub 2014 Dec 15. Research Support, Non-U.S. Gov't