HeLa: Stumpf 2013 Track Settings
 
Ribo-seq unique mappers from HeLa cells at different stages of the cell cycle (Stumpf et al. 2013)   (All Elongating Ribosomes (Footprints) tracks)



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 HeLa: All  All ribosome coverage data from HeLa cells in mitosis, S-phase and G1-phase (Stumpf et al. 2013)   schema 
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 HeLa: G1-phase  Ribosome profiles of elongating ribosomes from HeLa cells in G1-phase (Stumpf et al. 2013)   schema 
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 HeLa: M-phase  Ribosome profiles of elongating ribosomes from HeLa cells in M-phase (Stumpf et al. 2013)   schema 
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 HeLa: S-phase  Ribosome profiles of elongating ribosomes from HeLa cells in S-phase (Stumpf et al. 2013)   schema 

Description

This track contains data from Ribosomal sequence experiments carried out by Stumpf et al.(2013). Ribo-seq unique mapping was performed on HeLa cells for the three stages: mitotis, S-phase and G1-phase.

Methods

Raw sequence data were obtained from accession number (SRA099816). Data from the following samples were concatenated before processing:

SRR970593 and SRR970592 :mRNA profiles of mitotic HeLa cells

SRR970576 and SRR970578 :mRNA profiles of S-phase HeLa cells

SRR970550 and SRR970543 :mRNA profiles of G1 synchronized HeLa cells

Cutadapt was used to trim the adaptor sequence "CTGTAGGCACCATCAAT" from reads. An alignment to ribosomal RNA was then performed using Bowtie, and aligning reads were discarded. Finally, an alignment to the hg19 human genome was performed using RUM.

References

Craig R. Stumpf, Melissa V. Moreno, Adam B. Olshen, Barry S. Taylor and Davide Ruggero (2013). The Translational Landscape of the Mammalian Cell Cycle . Molecular Cell Volume 52, Issue 4, 574-582, 10 October 2013 10.1016/j.molcel.2013.09.018.