HFF:Stern-Ginossar 2012 Track Settings
 
HHV5 infection of human fibroblast cells (Stern-Ginossar 2012)   (All Elongating Ribosomes (Footprints) tracks)



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 All  All ribo-seq coverage data (Stern-Ginossar et al. 2012)   schema 
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 CHX 24hr  Ribo-seq unique mappers for cycloheximide treatment 24 hours post HHV5 infection (Stern-Ginossar 2012)   schema 
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 CHX 5hr  Ribo-seq unique mappers for cycloheximide treatment 5 hours post HHV5 infection (Stern-Ginossar 2012)   schema 
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 CHX 72hr  Ribo-seq unique mappers for cycloheximide treatment 72 hours post HHV5 infection (Stern-Ginossar 2012)   schema 
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 Control 5hr  Ribo-seq unique mappers for 5 hours post HHV5 infection (Stern-Ginossar 2012)   schema 
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 Control 72hr  Ribo-seq unique mappers for 72 hours post HHV5 infection (Stern-Ginossar 2012)   schema 
    

Description

These tracks show the coverage data for uniquely mapping reads to the human genome from ribosome profiling experiments on elongating ribosomes by Stern-Ginossar et al. (2012). In a set of experiments human fibroblasts were infected with human herpesvirus 5 strain Merlin and profiling was performed at 3 time points.

Methods

Raw sequence data were obtained from NCBI GEO database (Series GSE41605).

Cutadapt was used to trim the adaptor sequence "CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTGAA" from reads. An alignment to ribosomal RNA was then performed using Bowtie, and aligning reads were discarded. Finally, an alignment to both reference genomes (NCBI Reference Sequences:NC_006273 and GRCh37) was performed using RUM.

References

Stern-Ginossar, N., Weisburd, B., Michalski, A., Le, V. T. K., Hein, M. Y., Huang, S.-X., Ma, M., et al. (2012).Decoding human cytomegalovirus. Science (New York, N.Y.), 338(6110), 1088-93. doi:10.1126/science.1227919