HeLa: Niu 2013 Track Settings
 
N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. (Niu et al. 2013)   (All Elongating Ribosomes (Footprints) tracks)

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     Ribosome profiling SiControl RPF C1  Ribosome Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 
     Ribosome profiling SiControl RPF C5  Ribosome Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 
     Ribosome profiling SiYTHDF2 RPF C3  Ribosome Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 
     Ribosome profiling SiYTHDF2 RPF C8  Ribosome Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 

Description

PAR-CLIP and RIP was used to identify YTHDF2 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF2 siRNA knock-down

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP028325). Data from the following samples were processed:

Ribosome_profiling_SiYTHDF2_RPF_C8 Ribosome coverage data from Homo sapiens(Niu, et al. 2013)
Ribosome_profiling_SiYTHDF2_RPF_C3 Ribosome coverage data from Homo sapiens(Niu, et al. 2013)
Ribosome_profiling_SiControl_RPF_C5 Ribosome coverage data from Homo sapiens(Niu, et al. 2013)
Ribosome_profiling_SiControl_RPF_C1 Ribosome coverage data from Homo sapiens(Niu, et al. 2013)

Adapter sequence TGGAATTCTCGGGTGCC and ATCTCGTATGCCGTCTT 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.

References

Niu Y, Zhao X, Wu YS, Li MM, Wang XJ, Yang YG (2013) N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. . Genomics Proteomics Bioinformatics. 2013 Feb;11(1):8-17. doi: 10.1016/j.gpb.2012.12.002. Epub 2012 Dec 21. Research Support, Non-U.S. Gov't; Review