Description Ribosome profiling of elongating ribosomes using cycloheximide from HEK293 and HEK293Trex cells undergoing amino acid starvation or DOX treatment to induce eIF2-alpha expression (Gao et al. 2014). Methods
Raw sequence data were obtained from NCBI SRA database (SRA160745). Data from the following samples were processed:
| SRR1630831 | Ribo-Seq of HEK293 Cell (Control) |
| SRR1630832 | Ribo-Seq of HEK293/eIF2-alpha (S51D) Cell (Dox Treatment) |
| SRR1630833 | Ribo-Seq of HEK293 Cell (Amino Acid Starvation) |
Adaptor sequences were already removed from reads. An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. An alignment to the hg19 genome assembly was then performed using Bowtie, and this track contains the uniquely mapping reads that align to the A-site (using an offset of 15nt).
References
Gao, X., Wan, J., Liu, B., Ming, M., Shen, B., Qian, S.B. (2014). Quantitative profiling of initiating ribosomes in vivo. Nat Methods. doi: 10.1038/nmeth.3208.
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