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

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     Ribosome profiling SiControl input polyA C2  mRNA Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 
     Ribosome profiling SiControl input polyA C6  mRNA Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 
     Ribosome profiling SiControl input ribominus C7  mRNA Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 
     Ribosome profiling SiYTHDF2 input polyA C4  mRNA Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 
     Ribosome profiling SiYTHDF2 input polyA C9  mRNA Coverage of ribosomes from Homo sapiens (Niu et al. 2013)   Schema 
     Ribosome profiling SiYTHDF2 input ribominus C10  mRNA 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_input_ribominus_C10 mRNA-seq unique mappers from Homo sapiens(Niu, et al. 2013)
Ribosome_profiling_SiYTHDF2_input_polyA_C9 mRNA-seq unique mappers from Homo sapiens(Niu, et al. 2013)
Ribosome_profiling_SiYTHDF2_input_polyA_C4 mRNA-seq unique mappers from Homo sapiens(Niu, et al. 2013)
Ribosome_profiling_SiControl_input_ribominus_C7 mRNA-seq unique mappers from Homo sapiens(Niu, et al. 2013)
Ribosome_profiling_SiControl_input_polyA_C2 mRNA-seq unique mappers from Homo sapiens(Niu, et al. 2013)
Ribosome_profiling_SiControl_input_polyA_C6 mRNA-seq unique mappers 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