Fibroblast: Tirosh 2015 Track Settings
 
The transcription and translation landscapes during human cytomegalovirus infection reveal novel host-pathogen interactions (Tirosh et al. 2015)   (All mRNA-seq Reads tracks)

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     mRNA fibroblasts infected for 12hr  mRNA Coverage of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     mRNA fibroblasts infected for 24hr  mRNA Coverage of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     mRNA fibroblasts infected for 5hr  mRNA Coverage of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     mRNA fibroblasts infected for 72hr  mRNA Coverage of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     mRNA fibroblasts infected with irradiated virus  mRNA Coverage of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     mRNA uninfected fibroblasts  mRNA Coverage of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
    

Description

Ribosome profiling and mRNA-seq along HCMV infection.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP059531). Data from the following samples were processed:

mRNA_fibroblasts_infected_with_irradiated_virus mRNA-seq unique mappers from Homo sapiens(Tirosh, et al. 2015)
mRNA_fibroblasts_infected_for_12hr mRNA-seq unique mappers from Homo sapiens(Tirosh, et al. 2015)
mRNA_fibroblasts_infected_for_72hr mRNA-seq unique mappers from Homo sapiens(Tirosh, et al. 2015)
mRNA_fibroblasts_infected_for_5hr mRNA-seq unique mappers from Homo sapiens(Tirosh, et al. 2015)
mRNA_fibroblasts_infected_for_24hr mRNA-seq unique mappers from Homo sapiens(Tirosh, et al. 2015)
mRNA_uninfected_fibroblasts mRNA-seq unique mappers from Homo sapiens(Tirosh, et al. 2015)
mRNA_uninfected_fibroblasts_treated_with_type_1_interferon mRNA-seq unique mappers from Homo sapiens(Tirosh, et al. 2015)

Adapter sequence CTGTAGGCACCATCAAT 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 these tracks contains the uniquely mapping reads.

References

Tirosh O, Cohen Y, Shitrit A, Shani O, Le-Trilling VT, Trilling M, Friedlander G, Tanenbaum M, Stern-Ginossar N (2015) The transcription and translation landscapes during human cytomegalovirus infection reveal novel host-pathogen interactions . PLoS Pathog. 2015 Nov 24;11(11):e1005288. doi: 10.1371/journal.ppat.1005288. eCollection 2015.