BJ/MCF10A:Ji 2015 Track Settings
 
Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins (Ji et al. 2015)   (All mRNA-seq Reads tracks)

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     EH rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     EL rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     ELR rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     ERSrcEtOH01hr rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     ERSrcEtOH04hr rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     ERSrcEtOH24hr rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     ERSrcTAM00hr rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     ERSrcTAM01hr rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     ERSrcTAM04hr rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
     ERSrcTAM24hr rna  mRNA Coverage of ribosomes from Homo sapiens (Ji et al. 2015)   Schema 
    

Description

Ribosome profiling and RNA sequencing in two cancer cell models.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP054971). Data from the following samples were processed:

ERSrcTAM01hr_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
ERSrcTAM24hr_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
ERSrcTAM04hr_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
ERSrcTAM00hr_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
EH_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
ERSrcEtOH04hr_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
ERSrcEtOH01hr_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
ELR_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
EL_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)
ERSrcEtOH24hr_rna mRNA-seq unique mappers from Homo sapiens(Ji et al. 2015)

Adapter sequence CTGTAGGCACCATCAAT and AGATCGGAAGAGC 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

Ji Z.,Song R.,Regev A.,Struhl K. (2015) Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins . http://dx.doi.org/10.7554/eLife.08890.002