HEK293: Reid 2012 Track Settings
 
Ribosome profiles of elongating ribosomes from the cytosol and endoplasmic reticulum of HEK293 cells (Reid and Nicchitta 2012)   (All Elongating Ribosomes (A-site) tracks)



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 All  All ribosome profiling experiment data (Reid et al. 2012)   schema 
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 HEK293: Cytosol  Ribosome profiles of elongating ribosomes from the cytosol of HEK293 cells (Reid and Nicchitta 2012)    schema 
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 HEK293: ER  Ribosome profiles of elongating ribosomes from the endoplasmic reticulum of HEK293 cells (Reid and Nicchitta 2012)    schema 

Description

Ribosome profiles of elongating ribosomes from the cytosol and endoplasmic reticulum of HEK293 cells (Reid and Nicchitta 2012)

Methods

Raw sequence data were obtained from NCBI GEO database (Series GSE31539).

GSM782788HEK293_Cyt_footprints
GSM782786HEK293_ER_footprints

An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. Finally, an alignment to the hg19 genome assembly was performed using RUM, and this track contains the uniquely mapping reads that align to the A-site (using an offset of 15nt).

References

Reid, D. W., & Nicchitta, C. V. (2012). Primary Role for Endoplasmic Reticulum-bound Ribosomes in Cellular Translation Identified by Ribosome Profiling. The Journal of biological chemistry, 287(8), 5518-27. doi:10.1074/jbc.M111.312280