HeLa :Park 2016 Track Settings
 
Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. (Park et al. 2016)   (All Elongating Ribosomes (Footprints) 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  
     Asynchronous cell ribosome profiling  Ribosome Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 
     M phase ribosome profiling  Ribosome Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 
     M phase ribosome profiling synchronized by shake off  Ribosome Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 
     S phase ribosome profiling  Ribosome Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 

Description

HeLa cells were synchronized at S or M phase, and subject to RNA-seq, ribosome profiling and TAIL-seq analysis.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP072459). Data from the following samples were processed:

S_phase_ribosome_profiling Ribosome coverage data from Homo sapiens(Park, et al. 2016)
M_phase_ribosome_profiling Ribosome coverage data from Homo sapiens(Park, et al. 2016)
Asynchronous_cell_ribosome_profiling Ribosome coverage data from Homo sapiens(Park, et al. 2016)
M_phase_ribosome_profiling_synchronized_by_shake_off Ribosome coverage data from Homo sapiens(Park, et al. 2016)

Adapter sequence TGGAATTCTCGGGTGCC 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.

References

Park JE, Yi H, Kim Y, Chang H, Kim VN (2016) Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. . Mol Cell. 2016 May 5;62(3):462-71. doi: 10.1016/j.molcel.2016.04.007.