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

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     footprints fibroblasts infected for 12hr  Ribosome Profiles of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     footprints fibroblasts infected for 24hr  Ribosome Profiles of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     footprints fibroblasts infected for 5hr  Ribosome Profiles of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     footprints fibroblasts infected for 72hr  Ribosome Profiles of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     footprints fibroblasts infected with irradiated virus  Ribosome Profiles of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     footprints uninfected fibroblasts  Ribosome Profiles of elongating ribosomes from Homo sapiens (Tirosh et al. 2015)   Schema 
     footprints uninfected fibroblasts treated with type 1 interferon  Ribosome Profiles 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:

footprints_fibroblasts_infected_for_72hr Ribosome profiling data from Homo sapiens(Tirosh, et al. 2015)
footprints_fibroblasts_infected_for_24hr Ribosome profiling data from Homo sapiens(Tirosh, et al. 2015)
footprints_uninfected_fibroblasts_treated_with_type_1_interferon Ribosome profiling data from Homo sapiens(Tirosh, et al. 2015)
footprints_fibroblasts_infected_with_irradiated_virus Ribosome profiling data from Homo sapiens(Tirosh, et al. 2015)
footprints_fibroblasts_infected_for_5hr Ribosome profiling data from Homo sapiens(Tirosh, et al. 2015)
footprints_fibroblasts_infected_for_12hr Ribosome profiling data from Homo sapiens(Tirosh, et al. 2015)
footprints_uninfected_fibroblasts Ribosome profiling data 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.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.

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.