HeLa :Park 2016 Track Settings
 
Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. (Park et al. 2016)   (All mRNA-seq Reads 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 RNA seq  mRNA Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 
     M phase RNA seq oligo dT enriched  mRNA Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 
     M phase RNA seq ribozero treated  mRNA Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 
     M phase RNA seq synchronized by shake off  mRNA Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 
     S phase RNA seq oligo dT enriched  mRNA Coverage of ribosomes from Homo sapiens (Park et al. 2016)   Schema 
     S phase RNA seq ribozero treated  mRNA 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:

Asynchronous_cell_RNA_seq mRNA-seq unique mappers from Homo sapiens(Park, et al. 2016)
S_phase_RNA_seq_ribozero_treated mRNA-seq unique mappers from Homo sapiens(Park, et al. 2016)
M_phase_RNA_seq_oligo_dT_enriched mRNA-seq unique mappers from Homo sapiens(Park, et al. 2016)
M_phase_RNA_seq_ribozero_treated mRNA-seq unique mappers from Homo sapiens(Park, et al. 2016)
M_phase_RNA_seq_synchronized_by_shake_off mRNA-seq unique mappers from Homo sapiens(Park, et al. 2016)
S_phase_RNA_seq_oligo_dT_enriched mRNA-seq unique mappers 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.