HeLa:Zur 2016 Track Settings
 
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. (Zur et al. 2016)   (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  
     G1 Ribo Seq Exp1  Ribosome Profiles of elongating ribosomes from Homo sapiens (Zur et al. 2016)   Schema 
     G1 Ribo Seq Exp2  Ribosome Profiles of elongating ribosomes from Homo sapiens (Zur et al. 2016)   Schema 
     M Ribo Seq Exp1  Ribosome Profiles of elongating ribosomes from Homo sapiens (Zur et al. 2016)   Schema 
     M Ribo Seq Exp2  Ribosome Profiles of elongating ribosomes from Homo sapiens (Zur et al. 2016)   Schema 

Description

Two Ribo-Seq experiments, which included parallel RNA-Seq, one with 3 replicates, and the other with one replicate, totalling 4 technical replicates for the G1 and M phases of the cell cycle, respectively (totalling 16 samples), were performed.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP064313). Data from the following samples were processed:

M_Ribo_Seq_Exp1 Ribosome profiling data from Homo sapiens(Zur, et al. 2016)
M_Ribo_Seq_Exp2 Ribosome profiling data from Homo sapiens(Zur, et al. 2016)
G1_Ribo_Seq_Exp1 Ribosome profiling data from Homo sapiens(Zur, et al. 2016)
G1_Ribo_Seq_Exp2 Ribosome profiling data from Homo sapiens(Zur, et al. 2016)

Adapter sequence CTGTAGGCACCATCAAT and ATCTCGTATGCCGTCTT 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

Zur H, Aviner R, Tuller T (2016) Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. . Sci Rep. 2016 Feb 22;6:21635. doi: 10.1038/srep21635. Research Support, Non-U.S. Gov't