Monocytes :Su 2015 Track Settings
 
Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation. (Su et al. 2015)   (All Elongating Ribosomes (A-site) tracks)

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     IFNg RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Su et al. 2015)   Schema 
     Mock RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Su et al. 2015)   Schema 

Description

RPF and RNAseq libraries were generated from mock or IFN-g-primed human macrophages. Cells were stimulated with Pam3Cys and harvested at 4 hours. Libraries were generated using protocol modified from Illumina Truseq technology.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP056098). Data from the following samples were processed:

Mock_RPF Ribosome profiling data from Homo sapiens(Su, et al. 2015)
IFNg_RPF Ribosome profiling data from Homo sapiens(Su, et al. 2015)

Adapter sequence AAAAAAAAAAAAA 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 reads below 25nt were discarded. 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

Su X, Yu Y, Zhong Y, Giannopoulou EG, Hu X, Liu H, Cross JR, Ratsch G, Rice CM, Ivashkiv LB (2015) Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation. . Nat Immunol. 2015 Aug;16(8):838-49. doi: 10.1038/ni.3205. Epub 2015 Jun 29. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't