Lymphocytes: Reid 2015 Track Settings

Simple and inexpensive ribosome profiling analysis of mRNA translation. (Reid et al. 2015) (All Elongating Ribosomes (A-site) tracks)

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	lympho directExtract	Ribosome Profiles of elongating ribosomes from Homo sapiens (Reid et al. 2015)	Schema
	lympho pelleted	Ribosome Profiles of elongating ribosomes from Homo sapiens (Reid et al. 2015)	Schema

Description

Immortalized human lymphocytes were analyzed by ribosome profiling protocols with or without ribosome purification

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP057384). Data from the following samples were processed:

lympho_directExtract	Ribosome profiling data from Homo sapiens(Reid, et al. 2015)
lympho_pelleted	Ribosome profiling data from Homo sapiens(Reid, et al. 2015)

Adapter sequence AGATCGGAAGAGCACAC 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

Reid DW, Shenolikar S, Nicchitta CV (2015) Simple and inexpensive ribosome profiling analysis of mRNA translation. . Methods. 2015 Dec;91:69-74. doi: 10.1016/j.ymeth.2015.07.003. Epub 2015 Jul 8. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't