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
Raw sequence data were obtained from NCBI FTP directory(SRP028325). Data from the following samples were processed:
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.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.
| Ribosome_profiling_SiYTHDF2_RPF_C8 ||Ribosome profiling data from Homo sapiens(Niu, et al. 2013) |
| Ribosome_profiling_SiYTHDF2_RPF_C3 ||Ribosome profiling data from Homo sapiens(Niu, et al. 2013) |
| Ribosome_profiling_SiControl_RPF_C5 ||Ribosome profiling data from Homo sapiens(Niu, et al. 2013) |
| Ribosome_profiling_SiControl_RPF_C1 ||Ribosome profiling data from Homo sapiens(Niu, et al. 2013) |
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