Description Ribosome profiling assays were performed on cell lines treated with Harringtonine to generate data for validating translation initiatoin site prediction MethodsRaw sequence data were obtained from NCBI FTP directory(SRP066598). Data from the following samples were processed:
| GM19238_ribosome_protected_fragments | Ribosome profiling data from Homo sapiens(Raj, et al. 2016) |
| GM19204_ribosome_protected_fragments | Ribosome profiling data from Homo sapiens(Raj, et al. 2016) |
Adapter sequences had already been removed from reads. 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
Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK (2016) Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. . Elife. 2016 May 27;5. pii: e13328. doi: 10.7554/eLife.13328.
|
|