Description Two Ribo-Seq experiments, which included parallel RNA-Seq, one with 3 replicates, and the other with one replicate, totalling 4 technical replicates for the G1 and M phases of the cell cycle, respectively (totalling 16 samples), were performed. MethodsRaw sequence data were obtained from NCBI FTP directory(SRP064313). Data from the following samples were processed:
| M_Ribo_Seq_Exp1 | Ribosome profiling data from Homo sapiens(Zur, et al. 2016) |
| M_Ribo_Seq_Exp2 | Ribosome profiling data from Homo sapiens(Zur, et al. 2016) |
| G1_Ribo_Seq_Exp1 | Ribosome profiling data from Homo sapiens(Zur, et al. 2016) |
| G1_Ribo_Seq_Exp2 | Ribosome profiling data from Homo sapiens(Zur, et al. 2016) |
Adapter sequence CTGTAGGCACCATCAAT 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.
References
Zur H, Aviner R, Tuller T (2016) Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. . Sci Rep. 2016 Feb 22;6:21635. doi: 10.1038/srep21635. Research Support, Non-U.S. Gov't
|
|