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YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. (Shi et al. 2017)   (All Elongating Ribosomes (Footprints) tracks)

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     Ribosome profilingsiControlRPF  Ribosome coverage data from elongating ribosomes (SRR5099275) (Shi et al. 2017)   Schema 
     Ribosome profilingsiYTHDF3RPF  Ribosome coverage data from elongating ribosomes (SRR5099279, SRR5099277) (Shi et al. 2017)   Schema 

Description

Description fromGSE86214: We utilized PAR-CLIP triplicates and RIP replicates to identify binding sites and target transcripts of YTHDF3, and performed ribosome profling replicates to assess the consequences of YTHDF3 siRNA knock-down in HeLa cells.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP083699). Data from the following samples were processed:

Ribosome_profilingsiControlRPF Ribosome coverage data from elongating ribosomes Homo sapiens(Shi, et al. 2017)
Ribosome_profilingsiYTHDF3RPF Ribosome coverage data from elongating ribosomes Homo sapiens(Shi, et al. 2017)

Adapter sequence AGATCGGAAGAGCACAC and CAGATCGGAAGAGCACA 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 contain the uniquely mapping reads.,

References

Shi H, Wang X, Lu Z, Zhao BS, Ma H, Hsu PJ, Liu C, He C (2017) YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. .Cell Res. 2017 Mar;27(3):315-328. doi: 10.1038/cr.2017.15. Epub 2017 Jan 20.