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 profiles from elongating ribosomes Homo sapiens(Shi, et al. 2017) |
| Ribosome_profilingsiYTHDF3RPF | Ribosome profiles 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.
An offset of 15 nucleotides was then used to get the corresponding A-site of each read.These tracks contain the uniquely mapping reads.,ReferencesShi 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.
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