Description Ribosome profiling of lactimidomycin and cycloheximide treated HCT116 cells MethodsRaw sequence data were obtained from NCBI FTP directory(SRP042937). Data from the following samples were processed:
| Lactimidomycin_treated_HCT116 | Ribosome profiling data from Homo sapiens(Crappe, et al. 2015) |
Adapter sequence AGATCGGAAGAGCACAC 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 12 nucleotides was then used to get the corresponding P-site of each read.
References
Crappe J, Ndah E, Koch A, Steyaert S, Gawron D, De Keulenaer S, De Meester E, De Meyer T, Van Criekinge W, Van Damme P, Menschaert G (2015) PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration. . Nucleic Acids Res. 2015 Mar 11;43(5):e29. doi: 10.1093/nar/gku1283. Epub 2014 Dec 15. Research Support, Non-U.S. Gov't
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