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 Elongating Ribosomes (Footprints) tracks)

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

ERSrcTAM24hr_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcEtOH04hr_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcTAM04hr_harr Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ELR_harr Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ELR_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
EH_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcEtOH24hr_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcEtOH01hr_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcTAM01hr_harr Ribosome coverage data from Homo sapiens(Ji et al. 2015)
EL_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcTAM01hr_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
EL_harr Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcTAM04hr_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
EH_harr Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcTAM00hr_chx Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcTAM00hr_harr Ribosome coverage data from Homo sapiens(Ji et al. 2015)
ERSrcTAM24hr_harr Ribosome coverage data 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